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Rapid responses of bees and butterflies but not birds to targeted urban road verge habitat enhancements

Cities provide opportunities for biodiversity conservation through the design of urban greenspaces as wildlife habitat. A significant proportion of urban public land is narrow linear road verges, though their small size and harsh environmental conditions (e.g. high soil temperatures) may limit their ability to support plants and animals. We worked with a municipal government in a highly urbanised area to test whether conversion of standard road verges (e.g. lawn) to predominantly native understorey plants (forbs, grasses, and shrubs) selected for their abilities to tolerate harsh growing conditions and provide habitat increased the abundance and richness of bees, butterflies, and birds. We used a before-after-control-impact experiment and characterised temporal dynamics of biodiversity responses one year prior to planting and four years post planting. We also tested whether traits known to influence species responses to urbanisation (body size and feeding specialisation) mediated responses to road verge plantings. Bee species richness and abundance increased at experimental plantings in the first post-planting year and remained stable thereafter despite fluctuations at control sites. Butterfly abundance but not richness increased, and there was no evidence of bird responses to plantings. Larger bee species, which are known to be most negatively impacted by urbanisation, benefited more from the road verge plantings, while there was no effect of feeding specialisation. Bird and butterfly traits did not mediate responses to plantings. Synthesis and applications: Road verges comprise a significant proportion of urban green spaces, and our results suggest that despite their small sizes and harsh environmental conditions they can provide habitat for bees and to a lesser extent butterflies. We demonstrated that habitat value can be rapidly enhanced by converting standard road verges to native understorey plants, and that these benefits may be greatest for the bee species most negatively impacted by urbanisation. Modifications such as additional plant species or wider verges may be required for urban road verges to provide habitat for a greater range of taxa including birds and butterflies.

Responses of Pine Island and Thwaites glaciers to melt and sliding parameterizations

Pine Island and Thwaites glaciers are the two largest contributors to sea level rise from Antarctica. Here we examine the influence of basal friction and melt in determining projected losses. We examine both Weertman and Coulomb friction laws with explicit weakening as the ice thins to flotation, which many friction laws include implicitly via the effective pressure. We find relatively small differences with the choice of friction law (Weertman or Coulomb) but find losses are highly sensitive to the rate at which the basal traction is reduced as the area above the grounding line thins. Consistent with earlier work on Pine Island Glacier, we find sea level contributions from both glaciers vary linearly with the melt volume averaged over time and space, with little influence from the spatial or temporal distribution of melt. Based on recent estimates of melt from other studies, our work simulations suggest that melt-driven combined sea-level rise contribution from both glaciers is unlikely to exceed 10 cm by 2200. We do not include other factors, such as ice shelf breakup that might increase loss, nor factors such as increased accumulation and isostatic uplift that may mitigate loss.

Data from: Far red light increases maize volatile emissions in response to volatile cues from neighboring plants

Plants perceive the presence and defense status of their neighbors through light and volatile cues, but how plants integrate both stimuli is poorly understood. We investigated if and how low Red to Far red light (R:FR) ratios, indicative of shading or canopy closure, affect maize (Zea mays) responses to herbivore-induced plant volatiles (HIPVs), including the green leaf volatile (Z)-3-hexenyl acetate. We modulated light signaling and perception by using FR supplementation and a phyB1phyB2 mutant, and we determined volatile release as a response readout. To gain mechanistic insights, we examined expression of volatile biosynthesis genes, hormone accumulation, and photosynthesis. Exposure to a full blend of HIPVs or (Z)-3-hexenyl acetate induced maize volatile release. Short-term FR supplementation increased this response. In contrast, prolonged FR supplementation or constitutive phytochrome B inactivation in phyB1phyB2 plants showed the opposite response. Short-term FR supplementation enhanced photosynthesis and stomatal conductance and (Z)-3-hexenyl acetate-induced JA-Ile levels. We conclude that a FR-enriched light environment can prompt maize plants to respond more strongly to HIPVs emitted by neighbors, which might be explained by changes in photosynthetic processes and phytochrome B signaling. Our findings reveal interactive responses to light and volatile cues with potentially important consequences for plant-plant and plant-herbivore interactions.

Biaxial seismic response of base-column connections in sub-standard steel buildings: dataset

A complete dataset on the response of (semi-rigid and partial strength) column base plate connections in a substandard steel frame tested experimentally, are provided. Free-vibration, cyclic and pseudo-dynamic tests were carried out at the Structures Laboratory (STRULAB) of the University of Patras in the framework of H2020 EU-funded "Engineering Research Infrastructures for European Synergies (ERIES)" project.

Distribution, response to human disturbance, habitat preferences, and acoustic communication of tree hyraxes of Mt. Kilimanjaro, Tanzania

This data consists data from recordings done in Mt. Kilimanjaro. Hourly calls of tree hyraxes have been calculated between 19.00 until 06:00. Dataset also has variables collected by other research groups. We combined our data of cue count per hour with data to analyse tree hyrax density with explanatory variables to model occupancy of tree hyraxes in Kilimanjaro. Dataset was combined from several research projects conducted within the Kili-Project (Hemp et al. 2018) (Table 1). Variables included forest type, temperature (Appelhans et al. 2015) precipitation (Appelhans et al. 2016). diameter breast height (DBH), leaf density, max vegetation height, and leaf area index (LAI) (Rutten et al., 2015). We also included land use index (LUI) (Peters et al. 2019) to the dataset, which included four different variables (percentage plant biomass removal, agricultural inputs, modification of the vegetation and percentage of agricultural area in the surroundings). Abstract Limited knowledge exists of the distribution, habitat selection, behavior and response to human disturbance of many mammalian species from mountains of Africa. This is especially true for nocturnal mammals. We studied acoustically very active tree hyraxes (Dendrohyrax validus validus) from Mt. Kilimanjaro National Park, Tanzania mainly with bioacoustical methods. To gain understanding of the habitat preferences of tree hyraxes we combined bioacoustical data with botanical and meteorological data collected earlier by KiLi Project. According to GLMM analysis, disturbance caused by logging or forest fires significantly reduced tree hyrax calling activity. In Mt. Kilimanjaro, highest density of tree hyraxes was found from 2750 m a.s.l. It seems that extensive hunting in the past and selective logging below elevation 2500 m caused tree hyraxes to move up the mountain. Calls of tree hyraxes in Mt. Kilimanjaro resemble calls emitted by hyraxes in Taita Hills, Kenya; however, there are clear differences in their calling cultures. In Mt. Kilimanjaro tree hyraxes also sing songs, and their acoustic communication is very active and diverse. In most preferred habitats, groups of tree hyraxes may call 4500–5500 times during one night. Calling seem to have elements of turn taking and individual signatures. Future of tree hyraxes in large, 650 km2, Mt. Kilimanjaro National Park seems promising and perhaps in the future tree hyraxes will recolonize the whole park area again.

Data from: Foraging-induced craniofacial plasticity is associated with an early, robust, and dynamic transcriptional response

Phenotypic plasticity is the ability of a single genotype to vary its phenotype in response to the environment. Plasticity of the skeletal system in response to mechanical input is widely studied, but the timing of its transcriptional regulation is not well-understood. Here we used the cichlid feeding apparatus to examine the transcriptional dynamics of skeletal plasticity over time. Using three closely related species that vary in their ability to remodel bone and a panel of 11 genes, including well studied skeletal differentiation markers and newly characterized environmentally sensitive genes, we examined plasticity at 1, 2, 4 and 8 weeks following the onset of alternate foraging challenges. We found that the plastic species exhibited environment-specific bursts in gene expression at 1 week, followed by a sharp decline in levels, while the species with more limited plasticity exhibited consistently low levels of gene expression. This trend held across nearly all genes, suggesting that it is a hallmark of the larger plasticity regulatory network. We conclude that plasticity of the cichlid feeding apparatus is not the result of slowly accumulating gene expression difference over time, but rather is stimulated by early bursts of environment-specific gene expression followed by a return to homeostatic levels.

The bone marrow endothelial progenitor cell response to septic infection: Dataset

An early increase in the level of endothelial progenitor cells (EPCs) in the systemic circulation occurs in patients with septic infection/sepsis. The significance and underlying mechanisms of this response remain unclear. This study investigated the bone marrow EPC response in adult mice with septic infection induced by intravenous injection (i.v.) of Escherichia coli. For in vitro experiments, sorted marrow stem/progenitor cells (SPCs) including lineage(lin)-stem cell growth factor receptor(c-kit)+stem cell antigen-1(Sca-1)-, lin-c-kit+, and lin- cells were cultured with or without lipopolysaccharides (LPS) and recombinant murine vascular endothelial growth factor (VEGF) in the absence and presence of anti-Sca-1 crosslinking antibodies. In a separate set of experiments, marrow lin-c-kit+ cells from green fluorescence protein (GFP)+ mice, i.v. challenged with heat-inactivated E. coli or saline for 24 h were subcutaneously implanted in Matrigel plugs for 5 weeks. Marrow lin-c-kit+ cells from Sca-1 knockout (KO) mice challenged with heat-inactivated E. coli for 24 h were cultured in the Matrigel medium for 8 weeks. The marrow pool of EPCs bearing the lin-c-kit+Sca-1+VEGF receptor 2 (VEGFR2)+ (LKS VEGFR2+) and LKS CD133+VEGFR2+ surface markers expanded rapidly following septic infection, which was supported by both proliferative activation and phenotypic conversion of marrow stem/progenitor cells. An increase in marrow EPCs and their reprogramming for enhancing angiogenic activity correlated with cell-marked upregulation of Sca-1 expression. Sca-1 coupled with ras-related C3 botulinum toxin substrate 2 (Rac2) in signaling the marrow EPC response. Septic infection caused a substantial increase in plasma levels of IFN-γ, VEGF, G-CSF, and SDF-1. The early increase in circulating EPCs was accompanied by their active homing and incorporation into pulmonary microvasculature. These results demonstrate that the marrow EPC response is a critical component of the host defense system. Sca-1 signaling plays a pivotal role in the regulation of EPC response in mice with septic infection.

Incorporating plant phenological responses into species distribution models (SDMs) reduces estimates of future species loss and turnover

Anthropogenetic climate change has caused distribution shifts of many species, and species distribution models (SDMs) are central for documenting this relationship. However, most SDMs rarely consider the evolution of climate-sensitive functional traits, such as phenology, which strongly affect species fitness. Using >120,000 herbarium specimens representing 360 plant species across the eastern United States, we developed a novel "phenology-informed" SDM that integrates dynamic phenological responses to changing climates. Compared to standard SDMs, our phenology-informed SDMs forecast lower species habitat loss and less species turnover under climate change. These results suggest that phenotypic plasticity or local adaptation in phenology may help species adjust their ecological niches and persist in their habitats under rapid environmental change. Our findings reveal how phenology variation mediates species distributions and affects regional biodiversity patterns. Our newly developed model also circumvents the need for mechanistic models, facilitating the deployment of trait-based SDMs across unprecedented spatial and taxonomic scales.

Data from: Long-term climate and hydrologic regimes shape stream invertebrate community responses to a hurricane disturbance

Disturbances can produce a spectrum of short- and long-term ecological consequences that depend on complex interactions of the characteristics of the event, antecedent environmental conditions, and the intrinsic properties of resistance and resilience of the affected biological system. We used Hurricane Harvey's impact on coastal rivers of Texas to examine the roles of storm-related changes in hydrology and long-term precipitation regime on the response of stream invertebrate communities to hurricane disturbance. We detected declines in richness, diversity, and total abundance following the storm, but responses were strongly tied to direct and indirect effects of long-term aridity and short-term changes in stream hydrology. The amount of rainfall a site received drove both flood duration and flood magnitude across sites, but lower annual rainfall amounts (i.e., aridity) increased flood magnitude and decreased flood duration. Across all sites, flood duration was positively related to the time it took for invertebrate communities to return to a long-term baseline and flood magnitude drove larger invertebrate community responses (i.e., changes in diversity and total abundance). However, invertebrate response per unit flood magnitude was lower in sub-humid sites, potentially because of differences in refuge availability or ecological-evolutionary interactions. Interestingly, sub-humid streams had temporary large peaks in invertebrate total abundance and diversity following recovery period that may be indicative of the larger organic matter pulses expected in these systems because of their comparatively well-developed riparian vegetation. Our findings show that hydrology and long-term precipitation regime predictably affected invertebrate community responses and, thus, our work underscores the important influence of local climate to ecosystem sensitivity to disturbances.

Decoupling the rheological responses of a soft solid emulsion with liquid inclusions

Data used to write the paper Decoupling the rheological responses of a soft solid emulsion with liquid inclusions submitted to Journal of Physics: Condensed Matter for the Focus Issue on Materials with Liquid Inclusions (DOI: 10.1088/1361-648X/ad61ad)

Agronomic response and profitability of applying fractional doses of NPK fertilizer on cassava (Manihot esculenta Crantz) in Beni and Lubero territory, Democratic Republic of the Congo

Open the record for dataset details and reuse information.

Underlying REVISED dataset for the study: Singing and music making: Physiological responses across early to later stages of dementia

These files contain the REVIDED underlying data for the study, Singing and Music Making: Physiological Responses Across Early to Later Stages of Dementia; physiological data from Study 1 and Study 2, and video recording engagement scores from Study 2. in Study 2, the electrodermal readings (EDA) for the Slow Music readings in session 1 had become corrupted. The correct EDA data for this session was uploaded on 31.3.24. The project was funded by the Wellcome Trust as part of The Hub Award at the Wellcome Collection, London. The article that these data are based on can be here: https://wellcomeopenresearch.org/articles/6-150/v1, Wellcome Open Research, 6:150. The abstract from the accompanying article: Background: Music based interventions have been found to improve the wellbeing of people living with dementia.  Research to date has primarily used psychometric questionnaires and qualitative interviews to determine impact and efficacy. More recently there has been an interest in exploring if psychophysiological measures could provide additional information about how music, singing and other arts activities impact this population. Physiological responses can provide additional evidence about an individual’s experience of an activity and may be particularly useful for people who are experiencing difficulties with communication.  Methods: This multiple-case study design drew on previously collected, unanalysed archival data and explored the physiological responses of nine people with mild-to-moderate dementia during a singing group, and six people in the later stages of dementia during an interactive music group.  Medical grade Empatica E4 ™ wearable wristbands provided information on heart rate (HR), electrodermal activity (EDA), movement (ACC) and skin temperature (ST).  The interactive music group was video recorded using non-intrusive Fly 360-degree cameras™ in order to provide additional group interactive information about engagement.           Results: Physiological responses were analysed using simulation modelling analysis (SMA) within individual case studies.  Participants in the singing group showed an increase in EDA and HR as the session began.  HR and ST increased during faster paced songs.  EDA, movement and engagement were all higher during an interactive music group than during a control session (music listening). EDA and ST increased and in contrast to the responses during singing, HR decreased as the sessions began. EDA was higher during slower music, however this was less consistent in the more interactive intervention sessions than the control. There were no consistent changes in HR and movement responses during different styles of music.   Physiological responses peaked during familiar music, interactions, physical touch in addition to times that participants appeared disengaged.  Conclusion: Non-intrusive physiological measures obtained from easily worn wristband devices may provide valuable information about the experiences of people living with dementia who participate in arts and other activities, particularly for those in later stages when verbal communication may be more difficult and it is no longer possible to complete psychometric questionnaires. However, whenever feasible, they should be used in conjunction with other measures to develop a more nuanced understanding of these experiences.  Future research should consider using physiological measures with video-analysis and observational measures, where possible, to explore further how engagement in specific activities, wellbeing and physiology interact. This may provide valuable information for further development of activities and services for those living with dementias across different levels of impairment.

opencc-by-4.0Dec 2023View details →

Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment

When using any of this data, please cite the corresponding manuscript <div> <div> <a title="Rainer Kaiser et al., Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment.Sci. Adv.10,eadl1710(2024).DOI:10.1126/sciadv.adl1710" href="https://doi.org/10.1126/sciadv.adl1710">Rainer Kaiser et al., Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment. Sci. Adv. 10, eadl1710 (2024). DOI:10.1126/sciadv.adl1710</a> </div> </div> Original Data The following files contain all count data for the original data of this manuscript: sepsis1_raw_feature_bc_matrix.h5 -> raw feature barcode matrix for sepsis1 sequencing sepsis1_velocyto.loom -> velocyto matrices for sepsis1 sepsis2_raw_feature_bc_matrix.h5 -> raw feature barcode matrix for sepsis2 sequencing sepsis2_velocyto.loom -> velocyto matrices for sepsis2 sepsis_seurat.rds -> processed Seurat object containing original data cells. (Upd.: the meta.data-column "cellnames" contains the cell type annotation given in Figure 1B) Original Data Scripts process.R -> main analysis script functions.R -> helper functions for main analysis script enrichmentAnalysis.R -> script running the enrichment analysis process_wgcna.R -> script performing the wgcna analysis velocities_step1.R -> script performing velocity analysis (from seurat to data matrices) velocities_step2.py -> actual velocity analysis GSE137539 Re-Analysis gse137539_processed.Rds -> processed seurat object gse137539_process.R -> analysis script Bulk Analysis MOUSE_SEPTIC_SEPTICACT.inex.DirectDESeq2.xlsx-> Raw UMI counts (intronic+exonic from zUMIs) and DE genes MOUSE_SEPTIC_SEPTICACT.inex.DirectDESeq2.tsv.GeneOntology.BP.up.gsea.tsv -> Gene Set Enrichment Analysis on up-regulated genes using Gene Ontology Biological Process

opencc-by-4.0Apr 2024View details →

Diel greenhouse gas emissions demonstrate a strong response to vegetation patch types in a freshwater wetland

Data supporting submitted research paper. "All_flux_variables.csv" includes all plot data and is organized by the date/time of sample, campaign number, and sample location in rows and data collected as headers in the columns. "Flux_tower_data.csv" are meterological variables include in data analysis collected by a flux tower on sight. All other files are time series data for water pH (n = 2), water temperature (n = 3-5). Refer to the "metadata.csv" for units and descriptions of data in files.

opencc-by-4.0Apr 2024View details →

Response to Sea Surface Temperature and Primary Productivity to change in Earth's Orbit Eccentricity - Simulations

This dataset contains ocean and ocean biogeochemistry outputs from modeling experiments with present-day geography and various Earth's orbit confiurations. The set of simulation targets the role of Eccentricity on the tropical ocean sea surface temperature and primary productivity (Beaufort & Sarr, 2024) . The simulations have been run using the IPSL-CM5A2 General Circulation Model (Sepulchre et al. 2020 - IPSL-CM5A2 – an Earth system model designed formulti-millennial climate simulations, GMD) and offline version of PISCESv2 model (Aumont et al., 2015 - PISCES-v2: an ocean biogeochemical model for carbon and ecosystem studies, GMD). It includes 4 simulations. Data are monthly averages over the last 100 years of the simulations. Complementary outputs (4 simulations) can be found at https://www.seanoe.org/data/00728/84031/ (Beaufort et al., 2022)

opencc-by-4.0Dec 2022View details →

Dataset of the paper "Response of Sea Surface Temperature to Atmospheric Rivers"

Dataset of the paper "Response of Sea Surface Temperature to Atmospheric Rivers", whose manuscript will be submitted by 10/25/2023 The dataset contains the necessary data to generate the figures in the paper with the code in the link <a href="https://doi.org/10.5281/zenodo.10958491">https://doi.org/10.5281/zenodo.10958491</a> whose Github reference is <a href="https://github.com/meteorologytoday/paperfigures-2023-AR-SST-response">https://github.com/meteorologytoday/paperfigures-2024-AR-SST-response</a>

opencc-by-4.0Nov 2023View details →

F I G U R E 4 in Movement and habitat shift responses of juvenile Atlantic Salmon (Salmo salar) to annually permanent stream flooding

F I G U R E 4 Summary of Fulton's condition factor related to location, 2016–2017.

opencc-by-4.0Nov 2023View details →

F I G U R E 3 Mass specific growth rates among locations, 2016–2017 in Movement and habitat shift responses of juvenile Atlantic Salmon (Salmo salar) to annually permanent stream flooding

F I G U R E 3 Mass specific growth rates among locations, 2016–2017.

opencc-by-4.0Dec 2017View details →

Fig 2 in Birch Tree Response To Different Environmental And Meteorological Conditions In Lithuania

Fig 2. Changes in birch tree mortality (%) during the period of 1991-2014 (Forest monitoring data).