Find research datasets worth reusing

opencc-by-4.0Nov 2023View details →

3D cell tracking dataset of bacterial biofilm deformation and recovery under shear flow

This MAT file includes dataset in the scientific article "In vivo microrheology reveals elastic and plastic responses inside three-dimensional bacterial biofilms" by the following authors: Takuya Ohmura, Dominic Skinner, Konstantin Neuhaus, Gary Choi, Jörn Dunkel, Knut Drescher. This MAT file can be conveniently opened with Matlab. When you open this file with Matlab, you will find 4 variables stored in the file "Data_v3_loop2_newRxy_bidx1_274.mat"Variable 1: name_parameterNames of 31 parameters for columns in 3 variables: 'deformation_all', 'recovery_all' , 'plasticity_all'. The parameters have cell displacements, orientations, coordinates, biofilm indexes and experimental conditions. When the parameters have units, they are shown in the names. <ul><li>'x_Frame1[um]'</li><li>'y_Frame1[um]'</li><li>'z_Frame1[um]'</li><li>'Normalized_x_Frame1'</li><li>'Normalized_y_Frame1'</li><li>'Normalized_z_Frame1'</li><li>'LocalDensity_Frame1(VolumeFractionAround30px)'</li><li>'LocalCellNumberDensity_Frame1(VolumeFractionAround30px)'</li><li>'NematicOrderParameter_Frame1'</li><li>'AlignmentFlow_Frame1[rad]'</li><li>'AlignmentRadial_Frame1[rad]'</li><li>'AlignmentZaxis_Frame1[rad]'</li><li>'d_x[um]'</li><li>'d_y[um]'</li><li>'d_z[um]'</li><li>'Normalized_d_x'</li><li>'Normalized_d_y'</li><li>'Normalized_d_z'</li><li>'d_LocalDensity'</li><li>'d_LocalNumberDensity[um^-3]'</li><li>'d_NematicOrderParameter'</li><li>'d_AlignmentFlow[rad]'</li><li>'d_AlignmentRadial[rad]'</li><li>'d_AlignmentZaxis[rad]'</li><li>'CrossProduct[um^2]'</li><li>'BiofilmIndexNumber'</li><li>'Biofilm_width[um]'</li><li>'Biofilm_height[um]'</li><li>'Biofilm_volume[um^3]'</li><li>'FlowRate[ul/min]'</li><li>'Duration[min]'</li></ul>Variable 2: deformation_allThe rows indicate 704198 single-cell trackings in deformations of 274 bacterial biofilms. Each of the 274 bacterial biofilms has a different 'BiofilmIndexNumber'. The columns indicate 31 parameters which names are shown in 'name_parameter'.Variable 3: recovery_allThe rows indicate 685991 single-cell trackings in recoveries of 274 bacterial biofilms. Each of the 274 bacterial biofilms has a different 'BiofilmIndexNumber'. The columns indicate 31 parameters which names are shown in 'name_parameter'.Variable 4: plasticity_allThe rows indicate 665749 single-cell trackings in plasticities of 274 bacterial biofilms. Each of the 274 bacterial biofilms has a different 'BiofilmIndexNumber'. The columns indicate 31 parameters which names are shown in 'name_parameter'. To plot the cell tracked data in the figures of the article, use our MATLAB code uploaded in our GitHub (https://github.com/knutdrescher/biofilm-rheology).

opencc-by-4.0Nov 2023View details →

Targeted MAG recovery of novel Muirbacteria, Wallbacteria, Riflebacteria and Fusobacteria using SIngleM

Metagenome-assembled genomes (MAGs) from four underrepresented phyla, recovered using targeted analysis of metagenomes included in the <a href="sandpiper.qut.edu.au/">Sandpiper </a>website, analysed using <a href="https://github.com/wwood/singlem">SingleM</a>.

Groundwater level data, aquifer system boundaries, and supplementary tables associated with Jasechko, S. et al. Rapid groundwater decline and some cases of recovery in aquifers globally. Nature, doi.org/10.1038/s41586-023-06879-8 (2024).

Groundwater level data, aquifer system boundaries, and Supplementary Tables associated with Jasechko, S., Seybold, H., Perrone, D., Fan, Y., Shamsudduha, M., Taylor, R.G., Fallatah, O., Kirchner, J.W. Rapid groundwater decline and some cases of recovery in aquifers globally. Nature, https://doi.org/10.1038/s41586-023-06879-8 (2024).

Microbiome depletion and recovery in the sea anemone, Aiptasia, following antibiotic exposure

This provides data for the manuscript Microbiome depletion and recovery in the sea anemone, Aiptasia, following antibiotic exposure; 16smetadata.xlsx file used for in the DADA2 pipeline is provided, and the CFU count data is provided in cfu-counts-2022-01-20-modified.csv. The data for total protein content, pedal lacerate counts and algal abundance can all be found in the physio-2022-01-20.csv with the associated dataset (i.e. protein, algae, pedal lacerates) specified in the variable column.

State Comparison of Peer Recovery Worker Wages with Living Wages

ZipRecruiter provides real time data on wage offers by state. I compared mean wage offers with the Glasmeier's Living Wage Calculator. Because ZipRecruiter data are real time wage offers, they can change from month to month, I archived the state wage offer data from November 30, 2023. These data are entered into an Excel spreadsheet for comparisons with living wages. Because the living wage data in the 2023 calculator are based on 2022 dollars, I inflated living wages to 2022 dollars based on the rise in prices from mid-year 2022 to mid-year 2023.

Aboveground Biomass (AGB) in the Boreal Region: Dataset for Supporting Biomass Recovery Analysis

This package supplements the following paper submitted to Nature: Biomass recovery carbon gains surpass fire losses over boreal forests during the last decades. This dataset contains the Aboveground Biomass (AGB) map (unit: Mg/ha) for the boreal region in 2020 at ~100m resolution.The global AGB dataset, upon which this regional subset is based, was initially developed by Yu et al. (2023). The preprint version of the corresponding AGB data paper has been made available online and can be accessed at <a href="https://doi.org/10.5281/zenodo.7583611">https://doi.org/10.5281/zenodo.7583611</a>. This paper is currently under peer review. The AGB map for the boreal region, as featured in our Nature submission, is provided here for reference and further research.

opencc-by-4.0Mar 2024View details →

Selective recovery of boron, cobalt, gallium and germanium from seawater solar saltworks brines using N-methylglucamine sorbents: Column operation performance

The European Union (EU) identified a list of Critical Raw Materials (CRMs) crucial for its economy, aiming to find alternative sources. Seawater is a promising option as it contains almost all elements, although most at low concentrations. However, to the present, the CRMs' recovery from seawater is technically and economically unfeasible. Other alternatives to implement sea mining might be preferred, such as reverse osmosis brines or saltworks bitterns (after sodium chloride crystallisation). The CRMs' extraction in a selective way can be achieved using highly selective recovery processes, such as chelating sorbents. This study focuses on extracting Trace Elements (TEs) from solar saltworks brines, including boron, cobalt, gallium and germanium, using commercial N-methylglucamine sorbents (S108, CRB03, CRB05). The application of these sorbents has shown potential for boron recovery, but their selectivity for cobalt, gallium, and germanium requires further investigation. This research aims to assess these sorbents' kinetics and column mode performance for TEs recovery from synthetic bitterns. Boron and germanium were rapidly sorbed, reaching equilibrium (>90 %) within 1 h, except for S108, which took 2 h. In column mode, 20–25 pore volumes of bittern were treated to remove boron and germanium, but competition from other elements reduced treatment capacity. An acidic elution (1 M hydrochloric acid) allowed to elute them (>90 %), reaching concentration factors for germanium and boron of 35 and 11, respectively, while cobalt and gallium had less affinity for the sorbents. In addition, the experiments performed were fitted by a mass transfer model to determine the equilibrium constants and selectivities. Therefore, bittern mining has been proven as a secondary/alternative source to obtain CRMs, which can lead the EU to a position in which its dependence on other countries to obtain these raw materials would be decreased.

opencc-by-4.0Dec 2019View details →

Fig. 1 in Evidence of Stress Recovery in Free-Living Ciliate Colpoda cucullus: The Repair Capability of Resting Cysts to Damage Caused by Gamma Irradiation

Fig. 1. Excystment assay of Colpoda wet cysts (A) and dry cysts (B). 'Non-irradiated' indicates non-irradiated cysts; 'irradiated' indicates cysts irradiated at 4000 Gy, and 'irradiated-incubated' indicates cysts irradiated at 4000 Gy and incubated for 12 hours before the induction of excystment. Time indicates the number of hours after the induction of excystment. Columns and attached bars correspond to the means and standard errors, respectively, of six measurements. Asterisks and double asterisks represent significant differences at p <0.05 and p <0.01 (Mann-Whitney U test), respectively.

opencc-zeroApr 2024View details →

Data from: Sorting states of environmental DNA: Effects of isolation method and water matrix on recovery of membrane-bound, dissolved, and adsorbed states of eDNA

Environmental DNA (eDNA) once shed can exist in numerous states with varying behaviors including degradation rates and transport potential. In this study we consider three states of eDNA: 1) a membrane-bound state referring to DNA enveloped in a cellular or organellar membrane, 2) a dissolved state defined as the extracellular DNA molecule in the environment without any interaction with other particles, and 3) an adsorbed state defined as extracellular DNA adsorbed to a particle surface in the environment. Capturing, isolating, and analyzing a target state of eDNA provides utility for better interpretation of eDNA degradation rates and transport potential. While methods for separating different states of DNA have been developed, they remain poorly evaluated due to the lack of state-controlled experimentation. We evaluated the methods for separating states of eDNA from a single sample by spiking DNA from three different species to represent the three states of eDNA as state-specific controls. We used chicken DNA to represent the dissolved state, cultured mouse cells for the membrane-bound state, and salmon DNA adsorbed to clay particles as the adsorbed state. We performed the separation in three water matrices, two environmental and one synthetic, spiked with the three eDNA states. The membrane-bound state was the only state that was isolated with minimal contamination from non-target states. The membrane-bound state also had the highest recovery (54.11 ± 19.24 %), followed by the adsorbed state (5.08 ± 2.28 %), and the dissolved state had the lowest total recovery (2.21 ± 2.36 %). This study highlights the potential to sort the states of eDNA from a single sample and independently analyze them for more informed biodiversity assessments. However, further method development is needed to improve recovery and reduce cross-contamination.

opencc-zeroDec 2021View details →

Rapid ant community re-assembly in a Neotropical forest: recovery dynamics and land-use legacy

Regrowing secondary forests dominate tropical regions today, and a mechanistic understanding of their recovery dynamics provides important insights for conservation. In particular, land-use legacy effects on the fauna have rarely been investigated. One of the most ecologically dominant and functionally important animal groups in tropical forests are ants. Here, we investigated the recovery of ant communities in a forest – agricultural habitat mosaic in the Ecuadorian Chocó region. We used a replicated chronosequence of previously used cacao plantations and pastures with 1 – 34 years of regeneration time to study the recovery dynamics of species communities and functional diversity across the two land use legacies. We compared two independent components of responses on these community properties: resistance, which is measured as the proportion of an initial property that remains following the disturbance; and resilience, which is the rate of recovery relative to its loss. We found that compositional and trait structure similarity to old-growth forest communities increased with regeneration age, whereas ant species richness remained always at a high level along the chronosequence. Land-use legacies influenced species composition, with former cacao plantations showing higher resemblance to old-growth forests than former pastures along the chronosequence. While resistance was low for species composition and high for species richness and traits, all community properties had similarly high resilience. In essence, our results show that ant communities of the Chocó recovery rapidly, with former cacao reaching predicted old-growth forest community levels after 21 years and pastures after 29 years. Recovery in this community was faster than reported from other ecosystems and was likely facilitated by the low-intensity farming in agricultural sites and their proximity to old-growth forest remnants. Our study indicates the great recovery potential for this otherwise highly threatened biodiversity hotspot.

opencc-zeroDec 2021View details →

Zooplankton recovery from a whole‐lake disturbance: Examining roles of abiotic factors, biotic interactions, and traits

Community assembly following disturbance is a key process in determining the composition and function of the future community. However, replicated studies of community assembly at whole ecosystem scales are rare. Here, we describe a series of whole-lake experiments in which the recovery of zooplankton communities was tracked following an ecosystem-scale disturbance, i.e., application of the piscicide, rotenone. Using a BACI design, fourteen lakes in eastern Washington were studied: seven lakes were treated with rotenone, while seven lakes acted as reference systems. Each lake was monitored up to six months before and one to two years after the rotenone treatments. Zooplankton samples and environmental measurements were collected approximately monthly from each lake. Community responses following disturbance were assessed using metrics of abundance, diversity, and community composition, as well as taxonomic group abundance. Zooplankton recovery was also assessed using species traits related to habitat, feeding mode, trophic level, body size, and life history. In addition to patterns of recovery, potential mechanisms were explored relating to abiotic conditions, biotic interactions, and traits. There were steep declines in the abundance (average across years: 99%) and diversity (average across years: 75%) of the zooplankton community following rotenone treatment. Although abundance had recovered by the second year of the study, community diversity had not fully recovered after two years. Communities from rotenone lakes appeared to be compositionally recovered within about eight months following disturbance. Cyclopoid copepods were typically the first group to recover, and remained dominant for a few months, whereas cladocerans recovered more slowly, typically within ~6-7 months following rotenone. Calanoid copepods were not fully recovered two years after rotenone treatment. Traits related to body size and feeding mode were associated with the zooplankton communities following rotenone treatment. We failed to observe significant spatial synchrony in recovery patterns of zooplankton across lakes, though we did observe significant synchrony of zooplankton taxonomic groups within lakes. These findings suggest that traits related to ecological function, and to a lesser extent, biotic and abiotic factors, as well as characteristics of the disturbance itself, may be important in helping to understand recovery processes.

opencc-by-4.0Dec 2021View details →

Synthetic recovery of impulse propagation in myocardial infarction via silicon carbide semiconductive nanowires

DataSet for the publication "Synthetic recovery of impulse propagation in myocardial infarction via silicon carbide semiconductive nanowires" Pre-processed Confocal data for Figure 3 and Supplementary Figure 3. Acquired with Leica SP8 Laser-Scanning Confocal Microscope Pre-processed HPICM raw data for Figure 2, Supplementary Figure 2 Acquired with Ionscope Hopping Software Pre-processed double-patch clamp data for Figure 2b-c. Acquired with Clampfit 10.6 Pre-processed EP raw data for Figure 6-7-8, supplementary Figure 4. Acquired with Clampfit 10.6 Post-processed Kinematic trajectories for Supplementary Figure 5, Supplementary Figure 6 acquired with Video Spot Tracker V 8.00

opencc-by-4.0Apr 2020View details →

Data from: Drought and recovery effects on belowground respiration dynamics and the partitioning of recent carbon in managed and abandoned grassland

The supply of soil respiration with recent photoassimilates is an important and fast pathway for respiratory loss of carbon (C). To date it is unknown how drought and land-use change interactively influence the dynamics of recent C in soil respired CO2. In an in situ common-garden experiment, we exposed soil-vegetation monoliths from a managed and a nearby abandoned mountain grassland to an experimental drought. Based on two 13CO2 pulse-labelling campaigns, we traced recently assimilated C in soil respiration during drought, rewetting and early recovery. Independent of grassland management, drought reduced the absolute allocation of recent C to soil respiration. Rewetting triggered a respiration pulse, which was strongly fueled by C assimilated during drought. In comparison to the managed grassland, the abandoned grassland partitioned more recent C to belowground respiration than to root C storage under ample water supply. Interestingly, this pattern was reversed under drought. We suggest that these different response patterns reflect strategies of the managed and the abandoned grassland to enhance their respective resilience to drought, by fostering their resistance and recovery, respectively. We conclude that while severe drought can override the effects of abandonment of grassland management on the respiratory dynamics of recent C, abandonment alters strategies of belowground assimilate investment, with consequences for soil-CO2 fluxes during drought and drought-recovery.

opencc-by-4.0Mar 2022View details →

Dataset - Nasal microbiome disruption and recovery after mupirocin treatment in Staphylococcus aureus carriers and noncarriers

Background. Nasal decolonization procedures against the opportunistic pathogen Staphylococcus aureus rely on topical antimicrobial drug usage, whose impact on the nasal microbiota is poorly understood. We examined this impact in healthy S. aureus carriers and noncarriers.   Methods. This is a prospective interventional cohort study of 8 S. aureus carriers and 8 noncarriers treated with nasal mupirocin and chlorhexidine bath. Sequential nasal swabs were taken  over 6 months. S. aureus was detected by quantitative culture and genotyped using spa typing. RNA-based 16S species-level metabarcoding was used to assess the living microbial diversity.   Results. The species Dolosigranulum pigrum, Moraxella nonliquefaciens and Corynebacterium propinquum correlated negatively with S. aureus carriage. Mupirocin treatment effectively eliminated S. aureus, D. pigrum and M. nonliquefaciens, but not corynebacteria.   S. aureus recolonization in carriers occurred more rapidly than recolonization by the dominant species in noncarriers (median 3 vs. 6 months, respectively). Recolonizing S. aureus isolates had the same spa type as the initial isolate.   Conclusions. Mupirocin-chlorhexidine treatment had a long-lasting impact on the nasal microbiota. S. aureus recolonization predated microbiota recovery, emphasizing the strong adaptation of this pathogen   to the nasal niche and the transient efficacy of the decolonization procedure.

opencc-zeroApr 2022View details →

Data supporting: Success of post-fire plant recovery strategies varies with shifting fire seasonality

Wildfires are increasing in size and severity and fire seasons are lengthening, largely driven by climate and land use change. Many plant species from fire prone ecosystems are adapted to specific fire regimes corresponding to historical conditions and shifts beyond these bounds may have severe impacts on vegetation recovery and long-term species persistence. Here, we conduct a meta-analysis of field-based studies across different vegetation types and climate regions to investigate how post-fire plant recruitment, reproduction and survival are affected by fires that occur outside of the historical fire season. We find that fires outside of the historical fire season may lead to decreased post-fire recruitment for many species, particularly obligate seeding species. Conversely, we find a general increase of post-fire survival in resprouting species. Our results highlight the trade-offs that exist when considering the effects of changes in the seasonal timing of fire, an already present aspect of climate-related global fire regime change.

opencc-by-4.0Apr 2022View details →

Life cycle assessment of struvite recovery and wastewater sludge end-use: A Flemish illustration

This work was supported by the European Union's Horizon 2020 project Nutri2Cycle (Grant agreement No. 773682) and Interreg North-West Europe's ReNu2Farm (Grant: NEW601). These datasets are supplementary information to the manuscript titled <a href="https://www.sciencedirect.com/science/article/pii/S0921344922001732?via%3Dihub#!">"Life cycle assessment of struvite recovery and wastewater sludge end-use: A Flemish illustration"</a>

opencc-by-4.0Jul 2022View details →

DATASET: How decentralized treatment can contribute to the symbiosis between environmental protection and resource recovery

DATASET: How decentralized treatment can contribute to the symbiosis between environmental protection and resource recovery Science of The Total Environment, Volume 812, 15 March 2022, 151485 10.1016/j.scitotenv.2021.151485

opencc-by-4.0Jul 2022View details →

Dataset: Development and optimization of a bioelectrochemical system for ammonium recovery from wastewater as fertilizer

Dataset of Development and optimization of a bioelectrochemical system for ammonium recovery from wastewater as fertilizer <a href="https://doi.org/10.1016/j.clet.2021.100142">https://doi.org/10.1016/j.clet.2021.100142</a> <a href="https://www.sciencedirect.com/journal/cleaner-engineering-and-technology">Cleaner Engineering and Technology</a> <a href="https://www.sciencedirect.com/journal/cleaner-engineering-and-technology/vol/4/suppl/C">Volume 4</a>, October 2021, 100142

opencc-by-4.0Apr 2022View details →

Data/Code: Objective monitoring of functional recovery after total knee and hip arthroplasty using sensor-derived gait measures

Abstract Background: Inertial sensors hold the promise to objectively measure functional recovery after total knee (TKA) and hip arthroplasty (THA), but their value in addition to patient-reported outcome measures (PROMs) has yet to be demonstrated. This study investigated recovery of gait after TKA and THA using inertial sensors, and compared results to recovery of self-reported scores of pain and function. Methods: PROMs and gait parameters were assessed before and at two and fifteen months after TKA (n=24) and THA (n=24). Gait parameters were compared with healthy individuals (n=27) of similar age. Gait data were collected using inertial sensors on the feet, lower back, and trunk. Participants walked for two minutes back and forth over a 6m walkway with 180° turns. PROMs were obtained using the Knee Injury and Osteoarthritis Outcome Scores and Hip Disability and Osteoarthritis Outcome Score. Results: Gait parameters recovered to the level of healthy controls after both TKA and THA. Early improvements were found in gait-related trunk kinematics, while spatiotemporal gait parameters mainly improved between two and fifteen months after TKA and THA. Compared to the large and early improvements found in of PROMs, these gait parameters showed a different trajectory, with a marked discordance between the outcome of both methods at two months post-operatively. Conclusion: Sensor-derived gait parameters were responsive to TKA and THA, showing different recovery trajectories for spatiotemporal gait parameters and gait-related trunk kinematics. Fifteen months after TKA and THA, there were no remaining gait differences with respect to healthy controls. Given the discordance in recovery trajectories between gait parameters and PROMs, sensor-derived gait parameters seem to carry relevant information for evaluation of physical function that is not captured by self-reported scores.