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opencc-zeroFeb 2022View details →

Adaptive divergence generates distinct plastic responses in two closely related Senecio species

The evolution of plastic responses to external cues allows species to maintain fitness in response to the environmental variation they regularly experience. However, it remains unclear how plasticity evolves during adaptation. To test whether distinct patterns of plasticity are associated with adaptive divergence, we quantified plasticity for two closely related but ecologically divergent Sicilian daisy species (Senecio, Asteraceae). We sampled c.40 representative genotypes of each species from their native range on Mt Etna and then reciprocally transplanted multiple clones of each genotype into four field sites along an elevational gradient that included the native elevational range of each species, and two intermediate elevations. At each elevation we quantified survival and measured leaf traits that included investment (specific leaf area), morphology, chlorophyll fluorescence, pigment content and gene expression. Traits and differentially expressed genes that changed with elevation in one species often showed little change in the other species, or changed in the opposite direction. As evidence of adaptive divergence, both species performed better at their native site and better than the species from the other habitat. Adaptive divergence is therefore associated with the evolution of distinct plastic responses to environmental variation, despite these two species sharing a recent common ancestor.

Data of " Micromechanical characterization of the material response in a PA12-SLS fabricated lattice structure and its correlation with bulk behavior"

<pre>Data related to the publication (we would be grateful if you could cite the paper in the case in which you are using the data) title = "Micromechanical characterization of the material response in a PA12-SLS fabricated lattice structure and its correlation with bulk behavior", journal = "Polymer Testing", pages = " ", year = "2022", issn = "####", doi = "<a href="https://doi.org/10.1016/j.polymertesting.2022.107556">https://doi.org/10.1016/j.polymertesting.2022.107556</a>", author = "L. Cobian, M. Rueda-Ruiz, J.P. Fernandez-Blazquez, V. Martinez, F. Galvez, F. Karayagiz, T. Lück, J. Segurado, M.A. Monclus"</pre> This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 862015

opencc-zeroFeb 2022View details →

Data from: The Matthew effect: common species become more common and rare ones become more rare in response to artificial light at night

Artificial light at night (ALAN) has been and still is rapidly spreading, and has become an important component of global change. Although numerous studies have tested its potential biological and ecological impacts on animals, very few studies have tested whether it affects alien and native plants differently. Furthermore, common plant species, and particularly common alien species, are often found to benefit more from additional resources than rare native and rare alien species. Whether this is also the case with regard to increasing light due to ALAN is still unknown. Here, we tested how ALAN affected the performance of common and rare alien and native plant species in Germany directly, and indirectly via flying insects. We grew five common alien, six rare alien, five common native and four rare native plant species under four combinations of two ALAN (no ALAN vs ALAN) and two insect-exclusion (no exclusion vs exclusion) treatments, and compared their biomass production. We found that common plant species, irrespective of their origin, produced significantly more biomass than rare species, and that this was particularly true under ALAN. Furthermore, alien species tended to show a slightly stronger positive response to ALAN than native species did (p = 0.079). Our study shows that common plant species benefited more from ALAN than rare ones. This might lead to competitive exclusion of rare species, which could have cascading impacts on other trophic levels and thus have important community-wide consequences, when ALAN becomes more widespread. In addition, the slightly more positive response of alien species indicates that ALAN might increase the risk of alien plant invasions.

opencc-by-4.0Feb 2021View details →

Finding Efficient Trade-offs in Multi-Fidelity Response Surface Modeling: Generated data files and figures

All data files and figures generated for the paper "Finding Efficient Trade-offs in Multi-Fidelity Response Surface Modeling". The code used to generate this is archived at <a href="https://doi.org/10.5281/zenodo.6123254">zenodo.org/record/6123254</a>

Stimulation, reduction and compensation growth, and variable phenological responses to spring and/or summer-autumn warming in Corylus taxa and Cornus sanguinea L.

Two datasets containing data from three Corylus taxa (Corylus avellana, Corylus maxima and intermediate forms) and from Cornus sanguinea. Plants, in a common garden setting, were subjected to a periodic warming experiment in a greenhouse environment in 2018.

opencc-by-4.0Jan 2022View details →

Data repository of Predictors of Social Response to COVID-19 among Health Care Workers Caring for Individuals with Confirmed COVID-19 in Jordan

The outbreak of COVID-19 forced public health authorities around the world to call for national emergency plans. Public responses, in form of social discrimination and stigmatizing behaviors, are increasingly being observed against confirmed individuals with confirmed COVID-19 and healthcare workers (HCWs) caring for those individuals. Hence, this study aimed to investigate the perception of social discrimination and coping strategies, and explore predictors of social discrimination and coping toward COVID-19 among HCWs and individuals with confirmed COVID-19. This study used a cross-sectional descriptive-comparative design to collect data using a convenience sample of 105 individuals with confirmed COVID-19 and 109 HCWs using a web-based survey format. In this study, individuals confirmed with COVID-19 reported a high level of social discrimination compared with HCWs (t = 2.62, p < .01). While HCWs reported high level of coping with COVID-19 compared with individuals with COVID-19 (t = -3.91, p < .001). Educational level, age, monthly income, and taking over-the-counter medication were predictors of social discrimination and coping with COVID-19 among HCWs and individuals confirmed with COVID-19. In conclusion, the findings showed individuals with confirmed COVID-19 were more likely to face social discrimination and HCWs perform better coping with COVID-19 than individuals with confirmed COVID-19.

dataset from paper with title: "Direct Phenological Responses but Later Growth Stimulation upon Spring and Summer/Autumn Warming of Prunus spinosa L. in a Common Garden Environment"

abstract of paper: "Future predictions of forest ecosystem responses are a challenge, as global temperatures will further rise in the coming decades at an unprecedented rate. The effect of elevated temperature on growth performance and phenology of three Prunus spinosa L. provenances (originating from Belgium, Spain, and Sweden) in a common garden environment was investigated. One-year-old seedlings were grown in greenhouse conditions and exposed to ambient and elevated temperatures in the spring (on average 5.6 °C difference) and in the late summer/autumn of 2018 (on average 1.9 °C difference), while they were kept hydrated, in a factorial design. In the following years, all plants experienced the same growing conditions. Bud burst, leaf senescence, height, and diameter growth were recorded. Height and radial growth were not affected in the year of the treatments (2018) but were enhanced the year after (2019), whereas phenological responses depended on the temperature treatments in the year of the treatments (2018) with little carry-over effects in the succeeding years. Spring warming enhanced more height growth in the succeeding year, whereas summer/autumn warming stimulated more radial growth. Spring warming advanced bud burst and shortened the leaf opening process whereas summer/autumn warming delayed leaf senescence and enlarged the duration of this phenophase. These results can help predict the putative shifts in species composition of future forests and woody landscape elements."

Adaptive immune response selects for increased body size - dataset

The dataset for the manuscript " Adaptive immune response selects for increased body size ". The dataset is packed in ZIP archive 'Dataset_Ejsmond_etal_2022.zip' with variables and description of variables saved in Matlab workspaces.

Raw Data for the article: Klebsiella pneumoniae Lipopolysaccharides Serotype O2afg Induce Poor Inflammatory Immune Responses Ex Vivo

Currently, Klebsiella pneumoniae is a pathogen of clinical relevance due to its plastic ability of acquiring resistance genes to multiple antibiotics. During K. pneumoniae infections, lipopolysaccharides (LPS) play an ambiguous role as they both activate immune responses but can also play a role in immune evasion. The LPS O2a and LPS O2afg serotypes are prevalent in most multidrug resistant K. pneumoniae strains. Thus, we sought to understand if those two particular LPS serotypes were involved in a mechanism of immune evasion. We have extracted LPS (serotypes O1, O2a and O2afg) from K. pneumoniae strains and, using human monocytes ex vivo, we assessed the ability of those LPS antigens to induce the production of pro-inflammatory cytokines and chemokines. We observed that, when human monocytes are incubated with LPS serotypes O1, O2a or O2afg strains, O2afg and, to a lesser extent, O2a but not O1 failed to elicit the production of pro-inflammatory cytokines and chemokines, which suggests a role in immune evasion. Our preliminary data also shows that nuclear translocation of NF-κB, a process which regulates an immune response against infections, occurs in monocytes incubated with LPS O1 and, to a smaller extent, with LPS O2a, but not with the LPS serotype O2afg. Our results indicate that multidrug resistant K. pneumoniae expressing LPS O2afg serotypes avoid an initial inflammatory immune response and, consequently, are able to systematically spread inside the host unharmed, which results in the several pathologies associated with this bacterium.

Raw Data for the article: Impaired anti-SARS-CoV-2 humoral and cellular immune response induced by Pfizer-BioNTech BNT162b2 mRNA vaccine in solid organ transplanted patients

SARS‐CoV‐2 vaccine is considered the primary health strategy able to end the current COVID‐19 pandemic. This viral infection impacts more severely solid organ transplant recipients (SOTRs) than general population, but the effect of vaccination in this subgroup of immunosuppressed patients is not known due to their exclusion from vaccination trials. Preliminary reports suggest a lower antibody production after BNT162b2 Pfizer/BioNTech mRNA‐vaccine,<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0001"> 1 </a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0002">2 </a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0003">3 </a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222937/#ajt16702-bib-0004">4 </a>but no data are currently available on the elicited virus‐specific T cell responses.

opencc-by-4.0Jan 2022View details →

Vasculature Segmentation Validation Dataset - Part I - Simulated Tubes and Filter Responses

Dataset to allow exploration of data enhancement, segmentation, and validation for: https://www.biorxiv.org/content/10.1101/2020.07.21.213843v1 and associated future publications Dataset description: <ul> <li>SimulatedTubes: Computationally produced tubes (3 different sizes) that are hollow, filled, or filled with Gaussian distribution. To study filter responses, artificial noise and blurring were added.</li> <li>DataExFilterResponse: Example data of the head vasculature of 4dpf of zebrafish, where the response to different filters is tested (i.e. GF - general filtering and TF - tubular filtering / Sato enhancement; for TF also different scale sizes are examined; see also: https://www.mdpi.com/2313-433X/5/1/14).</li> </ul> Data acquisition: Experiments were performed according to the rules and guidelines of institutional and UK Home Office regulations under the Home Office Project Licence 70/8588 held by TC. Maintenance of adult zebrafish Tg(kdrl:HRAS-mCherry)s916 (Chi et al., 2008) was performed as described in standard husbandry protocols (Westerfield, 1993). Embryos, obtained from controlled mating, were kept in E3 medium buffer with methylene blue and staged as previously described (Kimmel et al., 1995). Embryos were embedded in 2% LMP-agarose with 0.01% Tricaine in E3 (MS-222, Sigma). Data were acquired using a Zeiss Z.1 light sheet microscope, Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, dual-side illumination with online fusion, activated Pivot Scan, image acquisition chamber incubation at 28°C, with a scientific complementary metal-oxide semiconductor (sCMOS) detection unit. Data properties can be summarised as: 16bit image depth, voxel dimensions in x, y and z of 1920 x 1920 x 400-600, respectively, giving a voxel size of 0.33 x 0.33 x 0.5 µm).  Contact: kugler.elisabeth[at]gmail.com Useful code links:  <ul> <li>https://github.com/ElisabethKugler/ZFVascularQuantification</li> <li>https://github.com/ElisabethKugler/Matlab3D-ImageAnalysis</li> </ul>

opencc-zeroFeb 2022View details →

Data from: Price equations for understanding the response of ecosystem function to community change

Biodiversity-ecosystem function research in natural ecosystems would benefit from new theoretical and analytical tools that match common characteristics of observational community data. To this end, we developed a novel, abundance-based version of the ecological Price equation in both discrete and continuous forms. As part of the presentation of this new method, we conducted two demonstration analyses. The first analysis focuses on pollination of watermelon by wild bees. We net-collected wild pollinator specimens from standard areas of flowering watermelon crop at 16 replicated farms in 2012. We also measured how many pollen grains each bee species deposited per visit. These per-visit pollen deposition rates were estimated as a genus-level property, as is common for landscape pollination studies. To determine total pollination for each bee species at each site, we multiplied pollinator visitation rates and per-visit pollen deposition. The attached data includes site by species matrices for the abundance (watermelon_com.csv) and per-capita pollen deposition (watermelon_fun.csv) of bee species. The second analysis focuses on changes in total community biomass of stream invertebrates collected from 25 sites along a strong, continuous pollution gradient. These data were previously published by Pomeranz et al. (2019), accessible at the Dryad link given below. Specimens were individually measured and assigned to one of six functional groups. Finer taxonomic resolution is available in the original study, but we use functional groups here to get enough data to effectively model. The attached data includes site by functional group matrices for the abundance (stream_inverts.csv) and per-capita biomass (stream_invert_size.csv) of stream invertebrate functional groups, and a third .csv which describes the level of pollution at each site (steam_data.csv). The code is a single R code file which produces the results and figures found in the manuscript. We have also included a README and several .csv files (those described above) that need to be read in. These data may be useful for other analyses of variation in ecosystem function across sites. We stress that the stream invertebrate data were collected by Pomeranz et al. (2019) and they should be cited for any use those data. The relevant link to access their data is: https://datadryad.org/stash/dataset/doi:10.5061/dryad.v6g985s

opencc-zeroMar 2022View details →

Data from 90-day quantitative inhalation toxicology study evaluating the dose-response and fate in the lung and pleura of chrysotile-containing brake dust

The final results from this multi-dose, 90-day inhalation toxicology study in the rat with life-time post-exposure observation have shown a significant fundamental difference in pathological response and tumorgenicity between brake dust generated from brake pads manufactured with chrysotile or from chrysotile alone in comparison to the amphiboles, crocidolite and amosite asbestos. The groups exposed to brake dust showed no significant pathological or tumorigenic response in the respiratory track compared to the air control group at exposure concentrations and deposited doses well above those at which humans have been exposed. Slight alveolar/interstitial macrophage accumulation of particles was noted. Wagner grades were 1–2 (1 = control group), similar to the TiO2 particle control group. Chrysotile was not biopersistent, exhibiting in the lung a deterioration of its matrix which results in breakage into particles and short fibers which can be cleared by alveolar macrophages and which can continue to dissolve. Particle-laden macrophage accumulation was observed, leading to a very-slight interstitial inflammatory response (Wagner grade 1–3). There was no peribronchiolar inflammation, occasional very-slight interstitial fibrosis (Wagner grade 4), and no exposure-related tumorigenic response. The pathological response of crocidolite and amosite compared to the brake dust and chrysotile was clearly differentiated by the histopathology and the confocal analysis. Crocidolite and amosite induced persistent inflammation, microgranulomas, persistent fibrosis (Wagner grades 4), and a dose-related lung tumor response. Confocal microscopy quantified extensive inflammatory response and collagen development in the lung, visceral and parietal pleura as well as pleural adhesions. These results provide a clear foundation for differentiating the innocuous effects of brake dust exposure from the adverse effects following amphibole asbestos exposure.

Supporting data for "The high-frequency tidal response of ocean worlds: Application to Europa and Ganymede"

Data files containing the static Love numbers that are used to compute the dynamic Love numbers.

Technology references in foundational accounts of Responsible Research and Innovation

Coding of references to different technology types within foundational accounts of Responsible Research and Innovation:  <ul> <li>Von Schomberg, R. (2013). A Vision of Responsible Research and Innovation. Responsible Innovation: Managing the Responsible Emergence of Science and Innovation in Society, 51–74. <a href="https://doi.org/10.1002/9781118551424.ch3">https://doi.org/10.1002/9781118551424.ch3</a></li> <li>Stilgoe, J., Owen, R., & Macnaghten, P. (2013). Developing a framework for responsible innovation. Research Policy, 42(9), 1568–1580. <a href="https://doi.org/10.1016/j.respol.2013.05.008">https://doi.org/10.1016/j.respol.2013.05.008</a></li> <li>European Commission. (2012a). Ethical and Regulatory Challenges to Science and Research Policy at the Global Level (KI-NA-25-101-EN-C). <a href="http://ec.europa.eu/research/science-society/document_library/pdf_06/ethical-and-regulatory-challenges-042012_en.pdf">http://ec.europa.eu/research/science-society/document_library/pdf_06/ethical-and-regulatory-challenges-042012_en.pdf</a></li> <li>European Commission. (2012b). Responsible Research and Innovation—Europe’s ability to respond to societal challenges (KI-31-12-921-EN-C). <a href="https://ec.europa.eu/research/swafs/pdf/pub_rri/KI0214595ENC.pdf">https://ec.europa.eu/research/swafs/pdf/pub_rri/KI0214595ENC.pdf</a></li> <li>van den Hoven, J. (2013). Value Sensitive Design and Responsible Innovation. In International handbook on responsible innovation. A global resource. John Wiley & Sons Inc.</li> <li>van den Hoven, J. (2017). The Design Turn in Applied Ethics. In J. van den Hoven, S. Miller, & T. Pogge (Eds.), Designing in Ethics (1st ed., pp. 11–31). Cambridge University Press. <a href="https://doi.org/10.1017/9780511844317.002">https://doi.org/10.1017/9780511844317.002</a></li> </ul> Reported in Novation (<a href="http://www.novation.inrs.ca/index.php/novation/article/view/10">link</a>). Methodology and definitions are set out in the Novation article.

opencc-zeroOct 2022View details →

Site fidelity and behavioral plasticity regulate an ungulate's response to extreme disturbance

1. With rapid global change, the frequency and severity of extreme disturbance events are increasing worldwide. The ability of animal populations to survive these stochastic events depends on how individual animals respond to their altered environments, yet our understanding of the immediate and short-term responses of animals to acute disturbances remains poor. 2. We focused on animal responses to the environmental disturbance created by megafire. Specifically, we explored the effects of the 2018 Mendocino Complex Fire in northern California, USA on the behaviour and body condition of black-tailed deer (Odocoileus hemionus columbianus). We predicted that deer would be displaced by the disturbance or experience high mortality post-fire if they stayed in the burn area. 3. We used data from GPS collars on 18 individual deer to quantify patterns of home range use, movement, and habitat selection before and after the fire. We assessed changes in body condition using images from a camera trap grid. The fire burned through half of the study area, facilitating a comparison between deer in burned and unburned areas. 4. Despite a dramatic reduction in vegetation in burned areas, deer showed high site fidelity to pre-fire home ranges, returning within hours of the fire. However, mean home range size doubled after the fire and corresponded with increased daily activity in a severely resource-depleted environment. Within their home ranges, deer also selected strongly for patches of surviving vegetation and woodland habitat, as these areas provided forage and cover in an otherwise desolate landscape. Deer body condition significantly decreased after the fire, likely as a result of a reduction in forage within their home ranges, but all collared deer survived for the duration of the study. 5. Understanding the ways in which large mammals respond to disturbance like wildfire is increasingly important as the extent and severity of such events increases across the world. While many animals are adapted to disturbance regimes, species that exhibit high site fidelity or otherwise fixed behavioural strategies may struggle to cope with increased climate instability and associated extreme disturbance events.

opencc-zeroMar 2022View details →

Data from: Tree growth responses to extreme drought after mechanical thinning and prescribed fire in a Sierra Nevada mixed-conifer forest, USA

An estimated 128 M trees died during the 2012-2016 California drought, largely in the southern Sierra Nevada Range. Prescribed burning and mechanical thinning are widely used to reduce fuels and restore ecosystem properties, but it is unclear if these treatments improve tree growth and vigor during extreme drought. This study examined tree growth responses after thinning, prescribed burning, and extreme drought at the Teakettle Experimental Forest, a historically frequent fire mixed-conifer forest in the southern Sierra Nevada of California, USA. Mechanical thinning (no thin, understory thin, and overstory thin) and prescribed burning (unburned, fall burning) were implemented in 2000-2001. Using annual growth data from increment cores, over 10,000 mapped and measured trees, and lidar-derived metrics of solar radiation and topographic wetness, we had two primary questions. First, what were the growth responses to thinning and prescribed burning treatments, and did these responses persist during the 2012-2016 drought? Second, what tree-level attributes and environmental conditions influenced growth responses to treatments and drought? Thinning increased residual tree growth and that response persisted through extreme drought 10 -15 years after treatments. Growth responses were higher in overstory versus understory thinning, with differences between thinning types more pronounced during drought. Species-specific growth responses were strongest with overstory thinning, with sugar pine (Pinus lambertiana) and incense-cedar (Calocedrus decurrens) having higher growth responses compared to white fir (Abies concolor) and Jeffery pine (Pinus jeffreyi). For individual trees, factors associated with higher growth responses were declining pretreatment growth trend, smaller tree size, and post-treatment low neighborhood basal area. Growth responses were initially not influenced by topography, but topographic wetness became important during extreme drought. Mechanical thinning resulted in durable increases in residual tree growth rates during extreme drought over a decade after thinning occurred, indicating treatment longevity in mitigating drought stress. In contrast, tree growth did not improve after prescribed burning, likely due to fire effects that reduced surface fuels, but had little effect on reducing tree density. Thinning treatments promoted durable growth responses, but focusing on stand-level metrics may ignore important tree-level attributes such as localized competition and topography associated with higher water availability. Mechanical thinning was effective at improving growth in trees that had been experiencing declining growth trends, but was less effective in improving growth responses in large old higher ecological importance.

Supplementary Table S5 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S5. Repository data showing genes identified by MapMan in Giza 178 in different pathways.  A, Cell wall modifications. B, Hemicellulose synthesis. C, Cellulose synthesis. D, Mannan-xylose-arabinose-fucose.  E, cell wall peroxidase. F, TF MYB.  G, bZIP.   H, Histone.

Supplementary Table S4 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S4. Repository data showing genes identified by MapMan in Giza 177 in different pathways.  A, Cell wall modifications. B, Hemicellulose synthesis. C, Cellulose synthesis. D, Mannan-xylose-arabinose-fucose. E, cell wall peroxidase. F, TF MYB.  G, bZIP.   H, Histone.

Supplementary Table S2 - Article:Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S2. Repository data for the global analysis produced for cv Giza 177.  A, Up regulated genes observed when comparing salt stressed plants vs unstressed controls.  B, Down regulated genes in Giza 177 observed when comparing salt stressed plants vs unstressed controls. C, Gene Ontology enrichment analysis (GOEA) results for Giza 177 up regulated genes.    D, GOEA results for Giza 177 down regulated genes.