Find research datasets worth reusing

opencc-by-4.0May 2021View details →

Dataset to "Hydrogen in tungsten trioxide by membrane photoemission and density functional theory modeling"

Dataset to "Hydrogen in tungsten trioxide by membrane photoemission and density functional theory modeling" as published in Physical Review B, 103 (2021), 205304

opencc-by-4.0Jul 2022View details →

Data from: Influence of the properties of different graphene-based nanomaterials dispersed in polycaprolactone membranes on astrocytic differentiation

Abstract Composites of polymer and graphene-based nanomaterials (GBNs) combine easy processing onto porous 3D membrane geometries due to the polymer and cellular differentiation stimuli due to GBNs fillers. Aimingto step forward to the clinical application of polymer/GBNs composites, this study performs a systematic and detailed comparative analysis of the influence of the properties of four different GBNs: i) graphene oxide obtained from graphite chemically processes (GO); ii) reduced graphene oxide (rGO); iii) multilayered graphene produced by mechanical exfoliation method (Gmec); and iv) low-oxidized graphene via anodic exfoliation (Ganodic); dispersed in polycaprolactone (PCL) porous membranes to induce astrocytic differentiation. PCL/GBN flat membranes were fabricated by phase inversion technique and broadly characterized in morphology and topography, chemical structure, hydrophilicity, protein adsorption, and electrical properties. Cellular assays with rat C6 glioma cells, as model for cell-specific astrocytes, were performed. Remarkably, low GBN loading (0.67 %wt.) caused an important difference in the response of the C6 differentiation among PCL/GBN membranes. PCL/rGO and PCL/GO membranes presented the highest biomolecule markers for astrocyte differentiation. Our results pointed to the chemical structural defects in rGO and GO nanomaterials and the protein adsorption mechanisms as the most plausible cause conferring distinctive properties to PCL/GBN membranes for the promotion of astrocytic differentiation. Overall, our systematic comparative study provides generalizable conclusions and new evidences to discern the role of GBNs features for future research on 3D PCL/graphene composite hollow fiber membranes for in vitroneural models.

opencc-by-4.0Jul 2022View details →

dataset for paper "Activation energy for pore opening in lipid membranes under an electric field"

Dataset for the paper "Electropermeabilization of hydroperoxidized lipid membranes". Data was generated from Orbit Mini miniaturized bilayer workstation (Nanion Technologies, Munich, Germany), with an inserted microelectrode cavity array (MECA 4) recording chip (Ionera Technologies, Freiburg, Germany). The data files have format .abf, a standard format for electrophysiological data.  It can be read by applications such as for instance - Clampex and ClampFit, from the patch-clamp software suite pCLAMP,  - Elements Data Analyzer, associated with the elements data reader software from Elements-IC,  or imported into Python through the package pyABF 2.3.5. import pyabf // abf=pyabf.ABF(path+"/"+f+"/"+abffile) // data = np.vstack((abf.sweepX, abf.data))  Data is organized in five folders named according to target hydroperoxidation degrees: POPC POPC-OOH 25% POPC-OOH 50% POPC-OOH 75% POPC-OOH 100% Inside each of the five above files data is organized by date, and informed with the actual measured hydroperoxidation degree for a given sample.

opencc-by-4.0Aug 2022View details →

Outputs of molecular dynamics simulations of two NS1 ZIKV variants in the membrane presence

Files corresponding to outputs obtained through Molecular Dynamics (MD) simulations of two Non-structural (NS) proteins 1 of the Zika virus from Uganda (ZIKV-UG) and Brazil (ZIKV-BR). Simulations were performed using GROMACS 5.1.5 or later versions.  Systems were built based on atomistic models (https://zenodo.org/record/5608521#.YvDNZTlBzJw) and converted to a coarse-grained representation employing MARTINI 2.2p ElNeDyn. It was assumed to be NS1 systems in apo and holo forms (i.e., in the absence and presence of a lipid bilayer, respectively). The membrane model tries to reproduce a lipid concentration of an endoplasmic reticulum lipid bilayer. Holo and apo systems were simulated until they reached 20 and 10 µs, respectively. Trajectories do not include water molecules. For the specific case of holo systems, frames were skipped every 5 frames, which means that processed trajectories are equivalent to simulations when it is recorded every 1000 ps. More details can be found at  <a href="https://doi.org/10.1021/acs.jcim.2c01461">https://doi.org/10.1021/acs.jcim.2c01461</a> Note: Some topology and index files important for MD analysis are also present.

Fig. 1 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane

Fig. 1 Schematic diagram illustrating the origin (a) and beginning of differentiation (b) of the oncospheral tegument and hook region membrane in the preoncospheral stage of embryonic development of Echinococcus multilocularis. All structures involved in formation of the oncospheral tegument and hook region membrane are marked in orange colour. Two red arrows show direction of progressive sinking or migration of the binucleate subtegumental perikaryon which sunk deep into the central region of differentiating oncosphere. HFC hook-forming cell or oncoblast, HP hook primordium, HRC hook region cavity, IE inner envelope, m mitochondria, N1, N2 two nuclei of the binucleate complex primordium, N nucleus of hook-forming cell, PBC binucleate complex primordium, V vesicles in the outer cytoplasm, undergoing progressive fusion

Fig. 6 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane

Fig. 6 TEM micrographs of mature eggs of Echinococcus multilocularis. a Part of the oncosphere showing the high concentration of beta-glycogen particles (β-gl) in the musculature of oncospheral hooks (HM) as indicated by the cytochemical test of Thiéry. b Low-power electron micrograph illustrating the general topography of mature intrauterine egg. Note: (1) a bilateral symmetry of the oncosphere (white interrupted line) and (2) position of hook region membrane and oncospheral tegument at one pole of the hexacanth. The hook region is marked by a frame composed of interrupted black lines. EmB embryophoric blocks, GC germinative cells, GL granular layer, HRM hook region membrane, IE inner envelope, LH lateral hooks, MH median hooks, OE outer envelope, OM oncospheral membrane, PG penetration glands, SC somatic cells

Fig. 5 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane

Fig. 5 High-power TEM micrographs showing ultrastructural details of the oncospheral tegument and hook region membrane. a Note two oblique sections of blades of the oncospheral hooks (HBl), surrounded by numerous long microvilli (Mv) which protrude into large cavity situated under the hook region membrane (HRM) and oncospheral membrane (OM). b Oblique section through the hook region membrane showing hook blade exit and oncospheral tegument with numerous long microvilli at its surface. DR desmosome rings, HM hook musculature, IE inner envelope

Fig. 4 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane

Fig. 4 Consecutive stages of a tegumental perikaryon migration. a Part of an embryo in the early preoncospheral stage of development showing much infolded oncospheral membrane and the binucleate perikaryon (BSP) of the oncospheral tegument in the early stage of its migration, sunken already below the peripheral layers of oncospheral musculature. b Part of the late stage of preoncospheral differentiation showing the binucleate perikaryon of oncospheral tegument sunk deep into the central part of the embryo and surrounded by differentiating blastomeres. H oncospheral hooks, HCF hook forming cell, HRM hook region membrane, IE inner envelope, N1, N2, nucleus, OE outer envelope, OM oncospheral membrane, SC somatic cells

opencc-by-4.0May 2024View details →

Dataset 2 for UV Plasmon-Enhanced Chiroptical Spectroscopy of Membrane-Binding Proteins, June 2024

Scanning electron microscopy images of Al nanostructures

opencc-by-4.0Jun 2024View details →

Molecular dynamics simulation of SpoIVFB:Pro-SigmaK complex ("pore water" added over membrane re-entrant loop)

Simulation originally starting with "pore water" above the membrane re-entrant loop. Found here are all files needed to reproduce or visualize the results of molecular dynamics simulation of the SpoIVFB intramembrane protease bound to the transcription factor Pro-sigmaK. The protein complex was embedded in a POPE_POPG_DAG_CL bilayer using CHARMM-GUI, and the "generate pore water" feature was used to initially fill the area above the membrane re-entrant loop with water (as opposed to lipids initially being placed in this vicinity). The system was equilibrated and and simulated using OpenMM. The README file is a C-shell script that will run equilibration and 250ns of unrestrained simulation.  Individual output (.out) and trajectory (.dcd) files are provided for each checkpoint of the simulation. A combined trajectory containing 250 ns of unrestrained simulation is also provided (combined_250ns_traj.dcd). Together with the step5_input.psf file, this combined dcd file can be used with common software such as VMD to visualize the molecular dynamics trajectory.

Fig. 3 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane

Fig. 3 Comparison of an early and advanced preoncospheral stage of embryonic development in Echinococcus multilocularis. a Ultrastructure of an embryo in the early preoncospheral stage of embryonic development. Note the binucleate complex primordium (PBC), which appears as a syncytial cap or "calotte" situated beneath the inner envelope (IE) at one pole of the developing embryo; two thick arrows mark the direction of progressive migration of both nuclei (N1, N2) surrounded by a thin layer of common cytoplasm and become transformed into the binucleate subtegumental perikaryon. b Part of the embryo in the advanced stage of preoncosphere showing the binucleate subtegumental perikaryon (BSP) of the tegumental syncytium sunk deep into the central part of the embryo and surrounded by differentiating blastomeres. Bl blastomere, C vitelline capsule, EmB embryophoric blocks, GL granular layer, H oncospheral hooks, HM hook muscles, HRM hook region membrane, KI keratin-like protein islands, MeN mesomere nucleus, OE outer envelope, OM oncospheral membrane, PG penetration gland, UW uterine wall

Fig. 2 in Echinococcus multilocularis (Cestoda, Cyclophyllidea, Taeniidae): origin, differentiation and functional ultrastructure of the oncospheral tegument and hook region membrane

Fig. 2 Schematic diagram illustrating the general topography of the oncospheral tegument and hook region membrane in relation to the oncospheral hooks, penetration gland arms and glandular exits in the mature intrauterine eggs. All structures involved in formation of the oncospheral tegument and hook region membrane are marked in orange colour. BSP binucleate subtegumental perikaryon, HRM hook region membrane, IE inner envelope LH lateral hooks, MH median hooks, Mv microvilli, N1, N2 nucleus, OT oncospheral tegument, PGA penetration glands arms

opencc-by-4.0Jun 2024View details →

Accompanying data for the paper "Accounting for the mechanical response of the cell membrane during the uptake of random nanoparticles"

<h2>Contributions</h2> <ul> <li>Iaquinta Sarah did contribute to the first draft edition, the development of the theoretical background of the algorithms and their implementation</li> <li>Khazaie Sharam did contribute to the revision and edition of the draft, and to the development of the theoretical background of the algorithms</li> <li>Jacquemin Frédéric did contribute to the project management and to the revision of the article.</li> <li>Fréour Sylvain did contribute to the project management and to the revision of the article.</li> </ul> <h2>Funding sources</h2> i-Site NExT : Grant/Award Number: ANR-16-IDEX-0007, Région Pays de la Loire and CNRS (French National Centre for Scientific Research). <h2>Data structure and information</h2> <ul> <li>code - <code>np_uptake source and data directory</code> <ul> <li>workflow - <code>scripts to reproduce figures</code></li> <li>np_uptake - <code>source code producing results and figures</code> <ul> <li>figures - <code>utility module to produce figures</code></li> <li>model - <code>see detailed description below</code></li> <li>metamodel_implementation - <code>see detailed description below</code></li> <li>sensitivity_analysis - <code>see detailed description below</code></li> </ul> </li> </ul> </li> </ul> <h3>Detailed description</h3> <h4>Abstract</h4> In order to improve the efficiency of the delivery of cancer treatments to cancer cells, the cellular uptake of nanoparticles (NPs), used as drug delivery systems, is numerically investigated through a mechanical approach. The objective is to optimize the NP's mechanical and geometrical properties to enhance their entry into cancer cells while avoiding benign ones. In previous studies, these properties are modeled as constant during the process of cellular uptake. However, recent observations of the displacement of the membrane's constituents towards the region in the cell membrane where the uptake of the NPs takes place show that the mechanical properties of the membrane vary during this process. Reason for writing The important contribution of adhesion to the wrapping process is already well documented in literature. It is therefore crucial to model this parameter properly as the conclusions made with a constant adhesion model may not be accurate compared to reality. Methodology Based on the existing knowledge on the reaction of membrane constituents to interaction with NPs, a 3-parameter sigmoidal function, accounting for the delay, amplitude, and speed of the reaction, has been used to model the evolution of adhesion. A variance-based sensitivity analysis has then been performed in order to quantify the influence of these parameters on the outputs of the model. Results It was found that the introduction of a variable adhesion tends to alter the predictions of endocytosis of NPs. The contribution of the amplitude and delay is respectively 0.32 and 0.43 times as important as that of the NP's aspect ratio, which is the prominent parameter. The influence of the slope of the transition is the least important parameter and does not appear to contribute to endocytosis. Implications Hence, models of the cellular uptake of NPs should use a variable, instead of constant, adhesion in order a representative as possible of the behavior of the cell membrane. The predictions are different from those obtained using a model with constant adhesion. <h4>Code</h4> This repository is divided into 4 folders: <ul> <li> model: contains the code used to compute the total variation of energy of the interface between a circular NP and a membrane by accounting for the mechanical accommodation of the latter. This folder also contains the routine to determine the final wrapping phase of the system. </li> <li> metamodel_implementation: contains a script to check for the representativeness of the dataset used to create a metamodel, a script to create Kriging and PCE metamodels using the Openturns opensource library, and a routine to validate the metamodel that has just been created; </li> <li> sensitivity_analysis: contains a script that allows to create samples based on the Kriging metamodels that have been created and exported as .pkl files in the metamodel folder. These samples are then used to the apply sensitivity algorithms. The user can choose among the various sensitivity algorithms provided by Openturns. For PCE metamodels, a routine is implemented to directly get the Sobol indices from the coefficients of the PCE metamodel. The indices can be plotted through plot routines; </li> <li> figures: contains a utils script to display the graphs and save them as PNG files with consistency. </li> </ul>

Figure 6 in Further investigation of the characteristics and biological function of Eimeria tenella apical membrane antigen 1

Figure 6. KEGG pathway classification of differentially expressed proteins in DF-1 cells transiently transfected with EtAMA1.

Figure 5 in Further investigation of the characteristics and biological function of Eimeria tenella apical membrane antigen 1

Figure 5. Gene ontology analysis of 163 proteins differentially expressed in DF-1 cells transiently transfected with EtAMA1. Proteins were annotated based on biological process, cellular component, and molecular function.

Figure 3 in Further investigation of the characteristics and biological function of Eimeria tenella apical membrane antigen 1

Figure 3. Inhibition of sporozoite invasion in vitro by antibodies against rEtAMA1, rEtESP, and rEtRON2. (a) Invasion-inhibition activities of single antibodies. Anti-rEtAMA1, rEtESP, and rEtRON2 rabbit anti-serum against recombinant EtAMA1, EtESP and EtRON2 protein, respectively; IgG, normal rabbit serum. (b) Invasion-inhibition activities of antibody combinations. Combinations of anti-rEtAMA1 and antirEtESP or anti-rEtRON2 were added at a ratio of 1:1 to generate a gradient concentration of IgG. All assays were performed in triplicate. *p <0.05, **p <0.01 and ***p <0.001, as determined by the Student's t-test versus the non-immunized IgG groups at the same concentration.

Figure 2 in Further investigation of the characteristics and biological function of Eimeria tenella apical membrane antigen 1

Figure 2. Colocalization of EtAMA1, EtESP, and EtRON2 in sporozoites by indirect immunofluorescence. Parasites were immunostained with anti-rEtAMA1, and anti-rEtESP or anti-rEtRON2 antibodies, visualized with FITC (green) and counter-stained with DAPI (blue). Scale bar, 10 µm.

Figure 1. EtAMA1 in Further investigation of the characteristics and biological function of Eimeria tenella apical membrane antigen 1

Figure 1. EtAMA1 is secreted by micronemes. (a) EtAMA1 secretion is FCS- and temperature-dependent. Fresh sporozoites were incubated in PBS or complete medium (CM) at 4 °C or 41 °C for 2 h. Supernatants containing excretory-secretory antigens (ESAs) were harvested and analyzed by western blotting to detect EtAMA1 and EtMIC2. (b) EtAMA1 secretion is inhibited by staurosporine. Sporozoites were incubated in CM with various concentrations of staurosporine or DMSO at 41 °C for 2 h. Supernatants containing ESAs was harvested and analyzed by western blotting to detect EtAMA1 and EtMIC2.

Figure 4 in Further investigation of the characteristics and biological function of Eimeria tenella apical membrane antigen 1

Figure 4. In vitro sporozoite invasion of DF-1 cells transiently transfected with EtAMA1. (a) Verification of pcDNA3.1-(+)-EtAMA1 expression in DF-1 cells by IFA. (b) The proliferation of DF-1 cells transfected with pcDNA3.1-(+)-EtAMA1 or pcDNA3.1-(+). (c) Sporozoite invasion rate in DF-1 cells transfected with pcDNA3.1-(+)-EtAMA1 or pcDNA3.1-(+). *p <0.05 and **p <0.01, as determined by the Student's t-test versus the untreated group.