Find research datasets worth reusing

opencc-by-4.0Apr 2024View details →

Data description: Deprivation of loading during early healing of rat Achilles tendons affects extracellular matrix composition and structure, and reduces cell density and cell alignment

<a name="_Hlk158643946"></a>Data description: Deprivation of loading during early healing of rat Achilles tendons affects extracellular matrix composition and structure, and reduces cell density and cell alignment Malin Hammerman, Maria Pierantoni, Hanna Isaksson *, Pernilla Eliasson * * joint last authors This dataset contains microscope images obtained from sections of healing and intact rat Achilles tendons undergoing different in vivo loading protocols and different time points post-transection. The data presented are the full resolution microscope images available in lower resolution in the accompanying manuscript’s Supplementary Figures 4-6. Each zipped folders contain images (tif-files) from all time-points for each respective staining and loading group.    <ul> <li>Col1: Sections stained with Collagen 1 antibodies</li> <li>Col3: Sections stained with Collagen 3 antibodies</li> <li>Elastin: Sections stained with Elastin antibodies</li> <li>Full_loading: Free cage activity</li> <li>Reduced_loading: Paralysis of the calf muscle with Botox</li> <li>Minimal_loading: Botox combined with joint fixation using a steel-orthosis</li> <li>Intact_reference: Contralateral uninjured Achilles tendons, used as reference</li> </ul> More description of the datasets inside the zipped files are available below and in the file 'Data Description.pdf'   Brief re-cap of methods Histological analysis was performed on healing Achilles tendons from Female Sprague-Dawley rats, specific-pathogen free (11-12 weeks, weight 299 ± 15 g), that had undergone full transection [13] of the right Achilles tendon, and been exposed to different levels of loading. Altered loading was imposed through two mechanisms. Reduced loading involved intramuscular Botox injections in the right calf muscles to induce plantar flexor muscle paralysis [24]. Additionally, the rats in the minimal loading group received a steel-orthosis around their right hindlimb directly after surgery [24]. Snap frozen tendons in OCT were sectioned longitudinally (7 μm thickness) and stained with immunofluorescent staining for collagen 1, collagen 3, or elastin. Sections were counterstained with DAPI followed by mounting. The tissue sections were imaged under a microscope (DMi8, Leica Microsystems, Wetzlar, Germany, with a Hamamatsu Orca LT Flash sCMOS camera) where fluorescence was detected at 550 nm (secondary antibody Alexa Fluor 594), 470 nm (secondary antibody Alexa Fluor 488) and 385 nm (DAPI), and exposure time was held constant for each color channel regarding magnification and staining. Mapping images of the entire tendon were obtained for one section per group (n=1 per healing time, loading group and ECM matrix protein). All images were adjusted to the negative control, where the primary antibody was omitted, to correct for unspecific antibody detection. Microscope images and description of file-names All data is presented in the form of .tif files. Please refer to the scale bars in the images. All image-files are named using the following abbreviations, as described below. As an example, the file name “Tendon_col1_FL_1W_col1.tif” refers to a tendon section stained for collagen 1 from a rat exposed to full loading for a period of 1 week after tendon transection, where only the channel for collagen 1 is shown, whereas “Tendon_col1_FL_1W_merged.tif” includes the channels for both staining for collagen 1 and DAPI of the same section. Col1: Sections stained with Collagen 1 antibodies Col3: Sections stained with Collagen 3 antibodies Elastin: Sections stained with Elastin antibodies dapi: Sections stained with 4',6-Diamidino-2-Phenylindole Dihydrochloride. FL:   Full loading (free cage activity), RL:   Reduced loading (paralysis of the calf muscle with Botox), ML:  Minimal loading (Botox combined with joint fixation using a steel-orthosis) IT:    Intact contralateral Achilles tendons, used as reference. 1W: Healing time point 1 week after transection 2W: Healing time point 2 weeks after transection 3W: Healing time point 3 weeks after transection 20W: Healing time point 20 weeks after transection Settings for brightness and contrast Collagen 1 1w FL 2000-12 000, UL 4000-10 000, ML 4000-12 000 2w FL 2500-10 000, UL 4000-10 000, ML 5000-12 000 3w FL 2000-12 000, UL 3500-13 000, ML 3500-14 000 12w FL 3000-12 000 20w FL 3000-11 000 IT 2000-8 000 Collagen 3 1w FL 3000-12 000, UL 4000-10 000, ML 4000-13 000 2w FL 2000 - 7 000, UL 2500-12 000, ML 2000-12 000 3w FL 2000-12 000, UL 3500-13 000, ML 3500-14 000 12w FL 3000-12 000 20w FL 2000-12 000 IT 3000-12 000 Elastin 1w FL 4000-10 000, UL 5000 - 8000, ML 3500-12 000 2w FL 3000-12 000, UL 3000-12 000, ML 3000-12 000 3w FL 2500-12 000, UL 2000-12 000, ML 2500-12 000, 12w FL 3500-12 000 20w FL 3500-12 000 IT 2000-12 000

opencc-by-4.0Sep 2021View details →

Data for "Transient Density-Induced Dipolar Interactions in a Thin Vapor Cell"

Data for "Transient Density-Induced Dipolar Interactions in a Thin Vapor Cell" as .npz files. The "datasets.csv" file lists, where each dataset is used in the journal publication. Additionally, there are two Python scripts (.py) which show how to load and plot a dataset. The dataset can be selected by changing the file name string in the script. Note, that for loading and plotting the simulation dataset the "plot_simulation.py" script has to be used.

opencc-by-4.0Nov 2018View details →

Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition

This repository contains code to accompany the manuscript titled Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition by Carly D. Kenkel and Line K. Bay   In this study, we used a phylogenetically controlled design to investigate the role of vertical symbiont transmission, an evolutionary mechanism predicted to enhance cooperation and holobiont fitness of reef-building corals. Six species of coral, three vertical transmitters and their closest horizontally transmitting relatives, were fragmented and subjected to a two-week thermal stress experiment. Symbiont cell density, photosynthetic function and translocation of photosynthetically fixed carbon between symbionts and hosts were quantified to assess changes in physiological metrics of fitness and cooperation. Amplicon sequencing of the Symbiodinium ITS-2 locus was used to investigate differences in symbiont community composition among focal species. We did not observe universally higher levels of cooperation in vertically transmitting species. However, the reduction in cooperation at the onset of bleaching was marginally associated with symbiont community diversity. Analysis of ITS2 amplicon sequence data suggest that it may not be vertical transmission per se that influences host-symbiont cooperation, but genetic uniformity of the symbiont community. Repository contents: <ul> <li> TraitDataAnalysis.R: Annotated R script for generating figures and re-creating statistical analyses <ul> <li> RsquaredGLMM.R: Accessory R script for running RsquaredGLMM analyses, called by TraitDataAnalysis.R </li> <li> NSF_RunningPam.csv: Input file for statistical analysis. Contains photophysiological data. Column headers are as follows: <ul> <li> Tank: Number of experimental tank in which experimental coral fragment was held </li> <li> Treatment: short-hand notation for sample treatments (e.g. ctrl1-5 = control temperature, genotypes 1-5) </li> <li> Water: source sump for temperature controlled water jackets for each set of treatment tanks </li> <li> Position: numerical rack position of coral fragment within experimental treatment tank </li> <li> Species: Coral species (Amil=A. millepora, Maqe=M. aequituberculata, Gast=G. astreata, Gach=G. acrhelia, Plob=P. lobata, Gcol=G. columna) </li> <li> Genotype: source colony origin of individual coral fragments within species </li> <li> Temp: experimental temperature treatment (ctrl: 27°C ; heat: 31°C) </li> <li> Treat: whether experimental corals received C14-labeled bicarbonate (bicarb), artemia or were sampled separately for Gene Expression Analysis (not presented in this manuscript) </li> <li> EQY: Effective quantum yield of Symbiodinium photosystem II as measured using PAM fluorometry </li> <li> Date: Actual calendar date of measure </li> <li> Transmission: coral symbiont transmission mode </li> <li> Reef: reef site of original coral collection </li> <li> Date: experimental date of measure </li> </ul> </li> <li> TraitData.csv: Input file for statistical analysis. Contains all physiological trait data. <ul> <li> Includes columns as described above for the Running_Pam file in addition to columns containing raw trait data as described in the manuscript. </li> </ul> </li> <li> TraitData_DaysAsCols.csv: Reformatted input file with trait data split by sampling day across columns </li> </ul> </li> <li> DADA2Analysis.R: Annotated R script for generating figures and running ITS2 amplicon analyses <ul> <li> GeoSymbio_ITS2_LocalDatabase_verForPhyloseq.fasta: FASTA file of the GeoSymbio ITS2 reference database <a href="https://sites.google.com/site/geosymbio/">https://sites.google.com/site/geosymbio/</a>, formatted for use with the R prograom Phyloseq </li> <li> SeqVars_6Feb.fasta: FASTA file of identified sequence variants resulting from DADA2 analysis </li> <li> OutputDADA_6Feb.csv: Counts of sequence variants by sample </li> <li> Raw FASTQ paired end read files can be downloaded from NCBI's SRA: PRJNA338365 </li> </ul> </li> </ul>

opencc-by-4.0Feb 2023View details →

Unit cells and resummed interactions for the calculations in "Systematic Analysis of Crystalline Phases in Bosonic Lattice Models with Algebraically Decaying Density-Density Interactions"

This directory contains all the unit cells with the respective resummed interactions used for the optimisation procedure to obtain the results in the work "Systematic Analysis of Crystalline Phases in Bosonic Lattice Models with Algebraically Decaying Density-Density Interactions[1]". To get an overview of the organization of the directory and a description of the data we recommend the README file. [1]: J. A. Koziol et al., Systematic Analysis of Crystalline Phases in Bosonic Lattice Models with Algebraically Decaying Density-Density Interactions, <a href="https://10.21468/SciPostPhys.14.5.136">10.21468/SciPostPhys.14.5.136</a>, 2023

zenodo40/100

Cilia density and flow velocity affect alignment of motile cilia from brain cells

Here we store the supplementary Materials and Methods for the publication Cilia density and flow velocity affect alignment of motile cilia from brain cells. In the Supplementary methods we included additional information on the hydrodynamic simulations.  Video1 and Video2 are videos referenced in the main text of the paper In the archive 'raw data and code.tar' , we provide raw images and codes to support the article.The complete dataset of raw images is more than 1 Tb. Here we are limited to 50Gb. The full dataset is available upon request. We choose to provide a full dataset of two culture at DIV 16, one treated with shear flow and a control without flow. For each of the two cultures, the videos with propelled particles are in the directory FL,  The bright field images without particles are stored in BF. Unfortunately we uploaded only few videos because of their large size. The results of the analysis of this dataset is reported in the directory analysis (available for each culture). Moreover we provide the code to analyse these data. The analysis routine: Step 1: for each field of view (fov) getting the cilia beating direction from the FL images. This is done with PIV. The code is Step1_PIVanalysis.mat Step 2: for each fov getting ciliated cell position and CBF from the BF movies. Gather the cilia beating direction and cilia posion and frequency in a unique figure and matlab class (Res.mat). This is done in Step2_gatherResults.mat The results of these analysis are stored in the analysis folder for each culture. These routines are repeated for each experiment and results are then plotted to get trends. In the folder code4figures we report the code that we used to make the figures in the papers starting from a matlab file "all_results*.mat", where are gathered all the analysis. The code may improve in the future with more comments. please check Nicola's github page for the latest update. Please contact us for any problem. https://github.com/NicolaPellicciotta/Code4-Cilia-density-and-flow-velocity-affect-alignment-of-motile-cilia-from-brain-cells All the raw videos and code are in the archive.

opencc-by-4.0Sep 2020View details →

zenodo40/100

Terminal density reversal and the role of Ca2+ in red blood cells clearance of healthy individuals

Density reversal of senescent red blood cells (RBCs) has been known for more than ten years, yet the identity of the candidate protein(s) is still elusive. While performing Percoll density gradient separation of RBCs from healthy individuals and their subsequent characterization, we identified a fraction of cells in the low-density fraction (~0.025% compared to total RBCs population) which shows reversal in their densities along with the characteristics of cellular senescence such as loss of membrane Band 3 protein and the phosphatidylserine exposure to the outer membrane leaflet. Our subsequent analysis showed that these cells are overloaded with Ca2+. We further measured intracellular [Na+] in individual RBCs by flow cytometry utilizing the dye CoroNa Green-AM.  Our findings showed that the cells with senescent characteristics lost their transmembrane Na+ gradient despite maintaining the membrane integrity. Consequently, these findings lead us to designate these cells as “senescent-like” cells. Our data further demonstrated altered activities of nonselective cation channels and pumps in these cells. In addition to a facilitated Na+ extrusion by Na+, K+-ATPase, our findings indicated altered ion transport via Piezo1 in these cells. Pharmacological modulation of Piezo1 with Yoda1/GsMTx4 showed that Piezo1 and, possibly, other nonselective cation channels by promiscuously transporting Na+ and Ca2+ play an important role in producing these low density “senescent like” cells.

opencc-by-4.0Jan 2022View details →

dryad40/100

In vitro cell cycle oscillations exhibit a robust and hysteretic response to changes in cytoplasmic density

Cells control the properties of the cytoplasm to ensure proper functioning of biochemical processes. Recent studies showed that cytoplasmic density varies in both physiological and pathological states of cells undergoing growth, division, differentiation, apoptosis, senescence, and metabolic starvation. Little is known about how cellular processes cope with these cytoplasmic variations. Here, we study how a cell cycle oscillator comprising cyclin-dependent kinase (Cdk1) responds to changes in cytoplasmic density by systematically diluting or concentrating cycling Xenopus egg extracts in cell-like microfluidic droplets. We found that the cell cycle maintains robust oscillations over a wide range of deviations from the endogenous density: as low as 0.2× to more than 1.22× relative cytoplasmic density (RCD). A further dilution or concentration from these values arrested the system in a low or high steady state of Cdk1 activity, respectively. Interestingly, diluting an arrested cytoplasm of 1.22× RCD recovers oscillations at lower than 1× RCD. Thus, the cell cycle switches reversibly between oscillatory and stable steady states at distinct thresholds depending on the direction of tuning, forming a hysteresis loop. We propose a mathematical model which recapitulates these observations and predicts that the Cdk1/Wee1/Cdc25 positive feedback loops do not contribute to the observed robustness, supported by experiments. Our system can be applied to study how cytoplasmic density affects other cellular processes.

opencc-zeroJan 2022View details →

dryad40/100

In vitro cell cycle oscillations exhibit a robust and hysteretic response to changes in cytoplasmic density

Open the record for dataset details and reuse information.

publicJan 2022View details →

opencc-by-4.0Apr 2020View details →

Well overviews of A549 spheroids at varying cell plating density and Matrigel concentrations

Above images depict well overviews of 5-day old A549 spheroid culture at varied cell plating density (1000,2000 and 3000 cells per well) and Matrigel density (10, 20 and 25 microliters). These were imaged using Perkin Elmer Opera Phenix High Content Screening System and were stained with a nuclear marker (Hoescht 33342) and an actin marker phalloidin/Alexa568.

opencc-by-4.0Apr 2020View details →

Well overviews of A549 spheroids at varying cell plating density and Matrigel concentrations

opencc-zeroJan 2021View details →

Data from: Egg mass polymorphism in Ambystoma maculatum is not associated with larval performance or survival, or with cell density of the algal symbiont Oophila amblystomatis

These data are from a 2018 study of larval morphology, performance, and survival in the spotted salamander (Ambystoma maculatum). We examined larvae of two egg mass color morphs: clear and white. We also quantified the density of algal (Oophila amblystomatis) cells on the egg capsules of embryos. The data correspond to our publication in Evolutionary Ecology.

opencc-by-4.0Jul 2022View details →

High-density electrode recordings reveal strong and specific connections between retinal ganglion cells and midbrain neurons.

This is the source file to be use for debugging problems on your own set-up. This files is a good example to both the repository provided for visual processing on the Kremow GitHub: https://github.com/KremkowLab/Axon-on-Neuropixels-in-Kilosort https://github.com/KremkowLab/tangential_recording

opencc-zeroAug 2022View details →

The role of cell-envelope synthesis for envelope growth and cytoplasmic density in Bacillus subtilis

All cells must increase their volumes in response to biomass growth to maintain intracellular mass density within physiologically permissive bounds. Here, we investigate the regulation of volume growth in the Gram-positive bacterium Bacillus subtilis. To increase volume, bacteria enzymatically expand their cell envelopes and insert new envelope material. First, we demonstrate that cell-volume growth is determined indirectly, by expanding their envelopes in proportion to mass growth, similarly to the Gram-negative Escherichia coli, despite their fundamentally different envelope structures. Next, we studied, which pathways might be responsible for robust surface-to-mass coupling: We found that both peptidoglycan synthesis and membrane synthesis are required for proper surface-to-mass coupling. However, surprisingly, neither pathway is solely rate-limiting, contrary to wide-spread belief, since envelope growth continues at a reduced rate upon complete inhibition of either process. To arrest cell-envelope growth completely, the simultaneous inhibition of both envelope-synthesis processes is required. Thus, we suggest that multiple envelope-synthesis pathways collectively confer an important aspect of volume regulation, the coordination between surface growth and biomass growth.

opencc-by-4.0Sep 2017View details →

Dataset: Quantifying cell densities and biovolumes of phytoplankton communities and functional groups using scanning flow cytometry, machine learning and unsupervised clustering

This dataset contains all relevant data for the manuscript (in submission) "Quantifying cell densities and biovolumes of phytoplankton communities and functional groups using scanning flow cytometry, machine learning and unsupervised clustering". Code written to analyse this dataset (which may be adapted for other flow cytometry datasets) is found at https://zenodo.org/record/999747 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Naming convention for raw flow cytometry data files (located in /Script 3. Generating raw data subset/input/): [Allparameters] _ [Year] - [Month] - [Date] [Hour] [u] [Minute] _ [Depth] e.g: Allparameters_2014-07-31 08u08_1.0m The date, time and depth indicate the location and time at which the measurement was taken.

opencc-zeroMay 2024View details →

From hidden hearing loss to supranormal auditory processing by neurotrophin 3-mediated modulation of inner hair cell synapse density

Loss of synapses between spiral ganglion neurons and inner hair cells (IHC synaptopathy), leads to an auditory neuropathy called hidden hearing loss (HHL) characterized by normal auditory thresholds but reduced amplitude of sound-evoked auditory potentials. It has been proposed that synaptopathy and HHL result in poor performance in challenging hearing tasks despite a normal audiogram. However, this has only been tested in animals after exposure to noise or ototoxic drugs, which can cause deficits beyond synaptopathy. Furthermore, the impact of supernumerary synapses on auditory processing has not been evaluated. Here, we studied mice in which IHC synapse counts were increased or decreased by altering neurotrophin 3 (Ntf3) expression in IHC-supporting cells. As we previously showed, postnatal Ntf3 knockdown or overexpression reduces or increases, respectively, IHC synapse density and suprathreshold amplitude of sound-evoked auditory potentials without changing cochlear thresholds. We now show that IHC synapse density does not influence the magnitude of the acoustic startle reflex or its prepulse inhibition. In contrast, gap-prepulse inhibition, a behavioral test for auditory temporal processing, is reduced or enhanced according to Ntf3 expression levels. These results indicate that IHC synaptopathy causes temporal processing deficits predicted in HHL. Furthermore, the improvement in temporal acuity achieved by increasing Ntf3 expression and synapse density suggests a therapeutic strategy for improving hearing in noise for individuals with synaptopathy of various etiologies.

opencc-by-4.0May 2024View details →

Secondary data_Cell density distributions histograms

Dataset containing secondary data regarding cell density. This data was used for the generation of histograms of cell density related to the article: The distinctive chemotactic responses of three marine herbivore protists to DMSP and related compounds. Therefore, provides information about the spatial distribution of three cultured dinoflagellates (Karlodinium armiger, Gyrodinium dominans and Oxyrrhis marina) responding to three chemical cues diffusing from a microcapillary.  Nomenclature: bin_edge_um: spatial postion (um2) / counts: cell/um2 (density9 / concentration: uM

opencc-by-4.0May 2020View details →

The effect of cell density on biomass and fatty acid productivity during cultivation of Rhodomonas salina in a tubular photobioreactor - the dataset.

The microalga Rhodomonas salina is widely used in aquaculture. There is a need for optimization of the growth of the microalgae and its content of essential fatty acids. Here, the fatty acid profile of Rhodomonas in relation to cell density during cultivation in a tubular PBR is investigated. It is expected that cell density is an important factor in controlling productivity and fatty acid content of the microalgae because cell density is important in determining light availability due to the self-shading of the algae. The carbon productivity as a function of cell density is described by a saturation curve. The carbon productivity and the productivity of total fatty acids are lowest at the lowest cell density, and independent of cell density at higher cell densities. The relative contribution of the two poly-unsaturated fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) increases with increasing cell density and saturates at 1 × 106 cells/ml. We conclude that large-scale production of Rhodomonas in this tubular PBR should take place at cell densities of 1 × 106 cells/ml, while there are indications for increasing difficulties in maintaining steady-state production in this PBR at higher cell densities.

opencc-by-4.0Oct 2024View details →

Development of a High-Energy-Density Lithiated Silicon-Sulfur Full Cell with Enhanced Stability and Longevity

The raw materials for the draft: "Development of a High-Energy-Density Lithiated Silicon-Sulfur Full Cell with Enhanced Stability and Longevity"

opencc-zeroJul 2021View details →

Robust surface-to-mass coupling and turgor-dependent cell width determine bacterial dry-mass density

During growth, cells must expand their cell volumes in coordination with biomass to control the level of cytoplasmic macromolecular crowding. Dry-mass density, the average ratio of dry mass to volume, is roughly constant between different nutrient conditions in bacteria, but it remains unknown whether cells maintain dry-mass density constant at the single-cell level and during non-steady conditions. Furthermore, the regulation of dry-mass density is fundamentally not understood in any organism. Using quantitative phase microscopy and a new image-analysis pipeline, we measured absolute single-cell mass and shape of the model organisms Escherichia coli and Caulobacter crescentus with improved precision and accuracy. We found that cells control dry-mass density indirectly, by expanding their surface, rather than volume, in direct proportion to biomass growth – according to a new surface growth law. At the same time, cell width is controlled independently. Therefore, cellular dry-mass density varies systematically with cell shape, both during the cell cycle or after nutrient shifts, while the surface-to-mass ratio remains nearly constant on the generation time scale. Transient deviations from constancy during nutrient shifts can be reconciled with turgor-pressure variations and the resulting elastic changes in surface area. Finally, we find that plastic changes of cell width after nutrient shifts are likely driven by turgor variations, demonstrating an important regulatory role of mechanical forces for width regulation. In conclusion, turgor-dependent cell width and a new, slowly varying surface-to-mass coupling constant are the independent variables that determine dry-mass density.