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Membrane modeling results from Surface Evolver
<h3>Summary</h3> <p>Three sets of membrane shapes of genus 0 generated in Surface Evolver (Brakke, 1992) are published here. </p> <p>The first set "ZS" reproduces the shapes that were published in Ziherl & Svetina (2005) (bi-layer energy with fixed integrated mean curvature, volume and area). In addition we report on energy values and deliver the shapes as .obj-files. The .dmp files are dumps from the Evolver runs, derived from Frickenhaus (2024).</p> <p>With the same approach, the second set "ST" was created, focusing on axisymmetric stick-like shapes, such as the UnduStick that has been investigated in detail in Frickenhaus & Wölper (2024). </p> <p>The third set "SC" deals with a Helfrich-flow energy functional, where instead of setting a mean curvature constraint, spontaneous curvature $H_0$ enters the bending energy functional.</p> <p>In all three sets energy minimization was done as much as possible, using Newton iteration (hessian_seek) along the surface normals, and gradient decent iterations until energy remained constant. The triangulation was adapted (see command macro gogo in .dmp files) by allowing tangential moves for some steps, equiangulation, vertex averaging, as well as edge length adaptation. File names may indicate non-equilibrium (-ne) or a saddle point (-saddle).</p> <p>Constraint target values are changed in a step-wise manner, writing out the complete data and macros for restarts after every step in a Surface Evolver dump-file automatically. Macros govu and gocu are for volume and curvature change, respectively. dv and dc are the corresponding volume/ curvature change per govo/ gocu cycle. If the triangulation becomes degenerate narrow, it may lead to automatic popping off (budding), i.e. seperation into two bodies. However, quantities volume, curvature and energy are not split up accordingly. </p> <p>The data was created during a project week on Scientific Programming at the University of Bremen, Germany (Mathematics, Summer 2024).</p> <h3>License/ Citation</h3> <p>The data is licensed CC-BY-4.0.</p> <p>When using the code, please cite appropriatly:</p> <p>Frickenhaus, S., Parmar, J. M., Mardomkhah, R., & Asadian, P. (2024). Membrane modeling results from Surface Evolver [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.12805964" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12805964</a></p> <h3>Contributions</h3> <p>RM and PA created the ZS data; JMP created the ST data, and SF created the SC data.</p> <h3>References</h3> <p>K.A. Brakke (1992) The Surface Evolver. Exp. Math. 1(2) <a href="https://dblp.org/db/journals/em/em1.html#Brakke92">https://dblp.org/db/journals/em/em1.html#Brakke92</a> 141-165</p> <p>P. Ziherl and S. Svetina (2005), Nonaxisymmetric phospholipid vesicles: Rackets, boomerangs, and starfish. EPL 70 690, <a href="https://doi.org/10.1209/epl/i2004-10527-4">doi: 10.1209/epl/i2004-10527-4</a></p> <p>S. Frickenhaus, (2024). Exploration of extreme vesicle shapes and their modular structure (1.0). Zenodo. <a href="https://doi.org/10.5281/zenodo.11199344" target="_blank" rel="noopener">doi: 10.5281/zenodo.11199344</a></p> <p>S. Frickenhaus, C. Wölper, (2024). MembraneR - a membrane modeling environment in R (Version 1). Zenodo. <a href="https://doi.org/10.5281/zenodo.12721406" target="_blank" rel="noopener">doi: 10.5281/zenodo.12721406</a></p>
Data from: Specific membrane capacitance, cytoplasm conductivity and instantaneous Young's modulus of single tumour cells
As label-free biomarkers, biophysical properties of cells are widely used for cell type classification. However, intrinsic biophysical markers, e.g. specific membrane capacitance (Cspecific membrane), cytoplasm conductivity (σconductivity) and instantaneous Young's modulus (Einstantaneous) measured for hundreds of single cells were not yet reported. In this study, single cells in suspension (adherent cells treated with trypsin) were aspirated through a microfluidic constriction channel at 25°C, and the entry processes and impedance profiles were recorded and translated to Cspecific membrane, σconductivity and Einstantaneous. Cspecific membrane, σconductivity and Einstantaneous of five cell types were quantified as 2.10±0.38 μF/cm2, 0.91±0.15 S/m and 5.52±0.95 kPa for H460 cells (ncell=437); 2.52±0.54 μF/cm2, 0.83±0.12 S/m and 5.54±1.04 kPa for H446 cells (ncell=410); 2.45±0.57 μF/cm2, 0.99±0.18 S/m and 5.16±1.68 kPa for A549 cells (ncell=442); 1.86±0.31 μF/cm2, 1.07±0.18 S/m and 3.86±0.81 kPa for 95D cells (ncell=415); 2.03±0.35 μF/cm2, 0.99±0.16 S/m and 3.49±0.70 kPa for 95C cells (ncell=290). The database of Cspecific membrane, σconductivity and Einstantaneous may serve as a reference for future studies of cellular biophysical properties.
Data from: Prognostic value of cerebral tissue oxygen saturation during neonatal extracorporeal membrane oxygenation
Objectives: Extracorporeal membrane oxygenation support is indicated in severe and refractory respiratory or circulatory failures. Neurological complications are typically represented by acute ischemic or hemorrhagic lesions, which induce higher morbidity and mortality. The primary goal of this study was to assess the prognostic value of cerebral tissue oxygen saturation (StcO2) on mortality in neonates and young infants treated with ECMO. A secondary objective was to evaluate the association between StcO2 and the occurrence of cerebral lesions. Study Design: This was a prospective study in infants < 3 months of age admitted to a pediatric intensive care unit and requiring ECMO support. Measurements: The assessment of cerebral perfusion was made by continuous StcO2 monitoring using near-infrared spectroscopy (NIRS) sensors placed on the two temporo-parietal regions. Neurological lesions were identified by MRI or transfontanellar echography. Results: Thirty-four infants <3 months of age were included in the study over a period of 18 months. The ECMO duration was 10±7 days. The survival rate was 50% (17/34 patients), and the proportion of brain injuries was 20% (7/34 patients). The mean StcO2 during ECMO in the non-survivors was reduced in both hemispheres (p = 0.0008 right, p = 0.03 left) compared to the survivors. StcO2 was also reduced in deceased or brain-injured patients compared to the survivors without brain injury (p = 0.002). Conclusion: StcO2 appears to be a strong prognostic factor of survival and of the presence of cerebral lesions in young infants during ECMO.
ArsR transcriptional regulator mediated attenuated mechanism by regulating self and outer membrane protein in Brucella
<p><span>The ArsR family transcriptional regulators are widely distributed in microorganisms, including in the important intracellular pathogen <i>Brucella</i>. ArsR proteins are implicated in numerous biological processes. However, the specific roles of ArsR family members in <i>Brucella</i> remain obscure. Here we show that ArsR3 (BSS2_RS07325) is required for <i>Brucella</i> survival both under stress <i>in vitro</i> conditions and in a murine infection model<i> in vivo</i>. ArsR3 autoregulate its own expression to maintain metal ion homeostasis to benefit bacterial survival. Moreover, ArsR3 also regulates the production of virulence factor outer membrane protein 25D (Omp25D) which is key for the survival of <i>Brucella</i> under stress conditions. Significantly, ArsR3 deletion strain attenuated in a murine infection model<i> in vivo</i>. Altogether, our findings reveal a unique mechanism in which the ArsR family member ArsR3 autoregulates its expression and also modulates Omp25D expression to maintain metal ion homeostasis and virulence in <i>Brucella</i>.</span></p>
Polymer–Lipid Hybrid Membranes as a Model Platform to Drive Membrane–Cytochrome c Interaction and Peroxidase-like Activity
<p>Data underlying the figures in the publication “Polymer–Lipid Hybrid Membranes as a Model Platform to Drive Membrane–Cytochrome c Interaction and Peroxidase-like Activity”, published in <em>J. Phys. Chem. B.,</em> <strong>2020</strong>, 124, 22, 4454–4465. <a href="https://pubs.acs.org/doi/10.1021/acs.jpcb.0c02727">https://pubs.acs.org/doi/10.1021/acs.jpcb.0c02727</a></p> <p>Table of contents:</p> <p><strong>1. Figure 1</strong>; Zip file containing the BAM images (<em>Figure 1b)</em> and excel files with the numerical data for the Langmuir isotherm graphs (<em>Figure 1a).</em></p> <p><strong>2. Figure 2, 5</strong>: Zip file containing the AFM images for the characterization of the solid-supported bilayers (<em>Figure 2</em>) and of the different membranes after protein insertion (<em>Figure</em> <em>5).</em> </p> <p><strong>3. Figure 4</strong>: Zip file containing the numerical data for <em>Figure 4,</em> showing the QCM-D plots of protein combination with supported membranes.</p> <p><strong>4. Figure 6</strong>: Zip file containing the numerical data for <em>Figure 6,</em> showing the qualitative comparison of protein activity by fluorimetric studies.</p>
Labelled Arabidopsis dataset for testing membrane segmentation models
<p>Labels of 3D dataset of confocal imaged arabidopsis for testing segmentation models.</p>
Arabidopsis dataset for testing membrane segmentation models
<p>3D dataset of confocal imaged arabidopsis for testing segmentation models.</p>
Figure 2 in Embryo retention, character optimization, and the origin of the extra-embryonic membranes of the amniotic egg
Figure 2. Distribution of random trees (out of 10,000) versus number of steps required by the distribution of developmental characters. (a) Character 1 (presence or absence of extended embryo retention). The reference tree requires three steps (*) for this character. (b) Character 2 (developmental stage at oviposition, with ordered states). The reference tree requires nine steps (*) for this character. Note that for both characters, many random trees require no more steps than the reference tree, thus implying that there is no phylogenetic signal in these characters.
Text-fig. 39. Scanning electron microscope (SEM) images of "Pollen clump with tricolpate pollen sp. 3"; Catefica locality, Portugal. a) Pollen clump, probably an anther fragment, containing one kind of pollen; b, d, e) Pollen grains from stamen fragment in polar (b, d) and equatorial (e) views showing the long colpi with coarsely verrucate aperture membranes; note the semitectate-reticulate tectum in the mesocolpium regions and foveolate-punctate tectum in the polar regions and along the aperture margins; c) Detail of pollen wall showing smooth muri and short, densely-spaced columellae. Specimen, Catefica 49-S107785 (a–e). Scale bars = 600 Μm (a), 6 Μm (b, d, e), 1.5 Μm (c). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 39. Scanning electron microscope (SEM) images of "Pollen clump with tricolpate pollen sp. 3"; Catefica locality, Portugal. a) Pollen clump, probably an anther fragment, containing one kind of pollen; b, d, e) Pollen grains from stamen fragment in polar (b, d) and equatorial (e) views showing the long colpi with coarsely verrucate aperture membranes; note the semitectate-reticulate tectum in the mesocolpium regions and foveolate-punctate tectum in the polar regions and along the aperture margins; c) Detail of pollen wall showing smooth muri and short, densely-spaced columellae. Specimen, Catefica 49-S107785 (a–e). Scale bars = 600 Μm (a), 6 Μm (b, d, e), 1.5 Μm (c).
Pure POPC Membrane with 650mM NaCl simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 77 NaCl, and 6400 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p>
Pure POPC Membrane with 350mM NaCl simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 41 NaCl, and 6400 SWM4 water molecules.</p> <p>The simulation have been performed using OpenMM 7.4.1</p> <p>Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong></p>
Pure POPC Membrane with 450mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM
<p>500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 52 CaCl2, and 6400 SWM4 water molecules. </p> <p>The simulation have been performed using OpenMM 7.4.1 Frames are saved in every 10 ps. Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset.</p> <p>wrapped.dcd has a frame saving frequency of 100 ps.</p> <p><strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong></p> <p><strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong></p> <p><strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were centered with VMD command "pbc wrap -center origin -centersel lipid -compound residue -all", concatenated and saved in xtc format with MDAnalysis.</strong></p> <p> </p>
Dataset of laboratory research of paper "Mutation Analysis and Characteristics of the 5T Allele in the Cystic Fibrosis Trans Membrane Gene"
<p>Dataset contains</p> <p>1. Blood Lymphocite</p> <p>2. Utensils and raw Materials</p>
Novel Use of a Gas Transfer Membrane Contactor Inhibits Legionella pneumophila Growth in Hot Water Systems
<p>Large Scale Hot Water Model System Measurement Data Summary</p>
5D-NP-FABTECH_FNH - Open Dataset for "Facile Handling of 3D Two-Photon Polymerized Microstructures by Ultra-Conformable Freestanding Polymeric Membranes"
<p>This is the open dataset for the paper: "Frank Marco den Hoed, Ottomaniello Andrea, Omar Tricinci, Luca Cesarecciu, Marco Carlotti, Patrizio Raffa and Virgilio Mattoli, Facile Handling of 3D Two-Photon Polymerized Microstructures by Ultra-Conformable Freestanding Polymeric Membranes, On line (2023) [DOI:10.5281/zenodo.7837976]".</p> <p>This include the Supplementary Information file ("Supplementary-Info-AdvFuncMater_denHoed-Ottomaniello_2023.pdf"), all the source material used for the paper preparation and more. </p> <p>For each folder (sub-dataset) there is a corresponding readme file describing the content and including metadata</p>
Supporting data for protein membrane simulations in "Recalibration of protein interactions in Martini 3"
<p>Coarse-grained molecular dynamics simulations of protein-membrane systems from "Recalibration of protein interactions in Martini 3". Simulations were run with the Martini 3.0 force field, along with two modified versions of Martini 3.0 in which the well-depth, ε, in the Lennard-Jones potential between all protein and water beads was rescaled by a factor <em>λ</em><sub>PW</sub>, ε in the Lennard-Jones potential between all protein beads was rescaled by a factor <em>λ</em><sub>PP</sub>. The simulation files are organized into one tar file for each rescaling approach. The simulation files are in xtc format, and are accompanied by a structure in gro format for system topology and a tpr file to start the simulation.</p>
Gallium-68 Prostate Specific Membrane Antigen PET in Diagnosing Patients With Thyroid Cancer
ClinicalTrials.gov study NCT03463889. IPD Sharing: NO. Countries: 1. Publications: 0.
Ozurdex for Diabetic Macular Edema Treated With Pars Plana vitrEctomy and Membrane RemovAl (OPERA Study)
ClinicalTrials.gov study NCT01613716. IPD Sharing: NO. Countries: 1. Publications: 0.
CopiOs® Pericardium Membrane for Localized Alveolar Ridge Augmentation
ClinicalTrials.gov study NCT00889265. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Comparison Tympanoplasty With Membrane Amniotic and Autologous Fascia
ClinicalTrials.gov study NCT03569969. IPD Sharing: UNDECIDED. Countries: 0. Publications: 7.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.