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1,491 results for “Ione”
Divalent cations bind to phosphoinositides to induce ion and isomer specific propensities for nano-cluster initiation in bilayer membranes
<p>We report all-atom molecular dynamics simulations of physiologically composed asymmetric bilayers containing phosphoinositides in the presence of monovalent and divalent cations. We have characterized the molecular mechanism by which these divalent cations interact with phosphoinositides. Calcium desolvates more readily, consistent with single-molecule calculations, and forms a network of ionic-like bonds that serve as a "molecular glue'' that allows a single ion to coordinate with up to three phosphatidylinositol-(4,5)-bisphosphate lipids. The phosphatidylinositol-(3,5)-bisphosphate isomer shows no such effect and neither does PI(4,5)P2 in the presence of Mg. The resulting network of Ca-mediated lipid-lipid bonds grows to span the entire simulation space and therefore has implications for the lateral distribution of phosophoinositides in the bilayer. We observe context-specific differences in lipid diffusion rates, lipid surface densities, and bilayer structure. The molecular-scale delineation of ion-lipid arrangements reported here provides insight into similar nanocluster formation induced by peripheral proteins to regulate the formation of functional signaling complexes on the membrane.</p>
Biomass material - undulating venus shell - supported nanoscale zero-valent iron for the adsorption of Pb2+ and Cd2+ ions in aqueous solution
<p>Nanoscale zero-valent iron (NZVI) has a high adsorption capacity for heavy metals, but easily forms aggregates. Herein, preprocessed undulating venus shell (UVS) is used as support material to prevent NZVI from reuniting. The SEM and TEM results show that UVS had a porous layered structure and NZVI particles were evenly distributed on the UVS surface. A large number of adsorption sites on the surface of UVS-NZVI are confirmed by IR and XRD. UVS-NZVI is utilized for adsorption of Pb<sup>2+</sup> and Cd<sup>2+</sup> at pH=6 in aqueous solution, and <a name="_Hlk35440679">the experimental maximum adsorption capacities are 29.91 mg·g<sup>-1</sup> and 38.99 </a>mg·g<sup>-1</sup>, respectively. Adsorption isotherm results indicate that the adsorption of ions by UVS-NZVI is more in line with the Langmuir model when Pb<sup>2+</sup> or Cd<sup>2+</sup> existed alone. For the mixed solution of Pb<sup>2+</sup> and Cd<sup>2+</sup>, only the adsorption of Pb<sup>2+</sup> by UVS-NZVI conforms to the Langmuir model. Kinetic studies demonstrate that the determination coefficients (R<sup>2</sup>) of the pseudo first-order kinetic model for UVS-NZVI adsorption of Cd<sup>2+</sup> and Pb<sup>2+</sup> are higher than those of the pseudo second-order kinetic model and Elovich kinetic model. Highly efficient performance for metal removal makes UVS-NZVI show potential application to heavy metal ion adsorption.</p>
Data from: Paleolimnological assessment of wildfire-derived atmospheric deposition of trace metal(loid)s and major ions to subarctic lakes (Northwest Territories, Canada)
<p>Wildfires release terrestrial elements to the atmosphere as aerosols, and these events are becoming more frequent and intense in the Arctic boreal forest as the climate is warming. We quantified the impact of atmospheric deposition of aerosols from local wildfires on metal(loid) fluxes using macroscopic charcoal accumulation rates, historical fire mapping, and element concentrations in <sup>210</sup>Pb‐dated lake sediment from five subarctic lakes with small catchments. Lake sediments showed small but significant increases in fluxes (median = 5–10%) for 22 trace metals, metalloids, or major ions following fire events. The impact of wildfire aerosols on element fluxes was mostly due to short‐term (≤2 years) increasing sedimentation rate (6 ± 41% increase), whereas sediment element concentrations were not strongly impacted. Wildfire‐associated deposition to lake sediments was mainly composed of Ca, Al, Fe, Mg, K, Mn, and Na, which are major constituents of ash from burned biomass, but changes in sediment flux were greatest for Sb, As, Ni, Ba, Mn, Mo, and Sr compared to pre‐disturbance conditions. Compared to anthropogenic sources of pollution, wildfire‐associated atmospheric fluxes of metal contaminants to the lakes (e.g., Hg, Pb, As, Sb, and Cd) were low. This study provides quantitative estimates of wildfire impacts on atmospheric geochemical fluxes to subarctic lakes, which can be used for modeling larger‐scale impacts under changing fire regimes.</p>
Data, analysis scripts, and simulations files for "Direct formation of nitrogen-vacancy centers in nitrogen doped diamond along the trajectories of swift heavy ions"
<p>Measured data and analysis script, as well as, simulated data, and input scripts for our publication "Direct formation of nitrogen-vacancy centers in nitrogen doped diamond along the trajectories of swift heavy ions"</p>
Simulation of Ion recirculation during -1 kV operation inside Inertial Electrostatic Confinement Fusion (IECF) device
<p>Ion phase space structure recorded during -1 kV cathode voltage indicating the re-circulation of ions across the cathode grid openings in a cylindrical Inertial Electrostatic Confinement Fusion (IECF) device.</p>
Direct Observational Evidence of the Simultaneous Excitation of Electromagnetic Ion Cyclotron Waves and Magnetosonic Waves by an Anisotropic Ring Distribution
<p>dataset of "Direct Observational Evidence of the Simultaneous Excitation of Electromagnetic Ion Cyclotron Waves and Magnetosonic Waves by an Anisotropic Proton Ring Distribution"</p>
Data and code for analysis of ion currents in mass spectrometric profiles using glioblastoma tissue
<p>This upload contains all replication material for "Analysis of ion currents in mass spectrometric profiles using glioblastoma tissue" (forthcoming).</p> <p><strong>Authors:</strong> E.S. Zhvansky, A.A. Sorokin, D.S. Zavorotnyuk, V.A. Shurkhay, D.S. Bormotov, A.A. Potapov.</p> <p><strong>Code and data are located within spectra_data_and_code.zip.</strong> Code is written in MATLAB R2019b.</p> <p>Please find the readme.txt for code using and the code to replicate the main findings of the paper (figures_replication.m).</p>
Ions release from hydroxyapatite and substituted hydroxyapatites in different immersion liquids: In vitro experiments and theoretical modelling study
<p>The multi-substituted hydroxyapatites (ms-HAPs) are currently gaining more consideration due to their multifunctional properties and biomimetic structure, owning thus an enhanced biological potential in orthopedic and dental applications. In this study, nano hydroxyapatite (HAP) substituted with multiple cations (Sr2+, Mg2+ and Zn2+) for Ca2+ and anion (SiO44-) for PO43- and OH-, specifically HAPc-5%Sr and HAPc-10%Sr (where HAPc is HAP-1.5%Mg-0.2%Zn-0.2%Si), both lyophilized noncalcined and lyophilized calcined, were evaluated for their in vitro ions release. These nanomaterials were characterized by SEM, FE-SEM and EDX, as well as by AFM images and by surface-specific areas and porosity. Further, the release of cations and of phosphate anions were assessed from nano HAP and ms-HAPs, both in water and in simulated body fluid (SBF), in static and simulated dynamic conditions, using inductively coupled plasma optical emission spectrometry (ICP-OES). The release profiles were analyzed and the influence of experimental conditions was determined for each of the six nanomaterials and for various periods of time. The pH of the samples soaked in the immersion liquids was also measured. The ions release mechanism was theoretically investigated using the Korsmeyer-Peppas model. The results indicated a mechanism principally based on diffusion and dissolution, with possible contribution of ion exchange. The surface of ms-HAP nanoparticles is more susceptible to dissolution into immersion liquids due to the lattice strain provoked by simultaneous multi-substitution in HAP structure. According to the findings, it is rational to suggest that both materials HAPc-5%Sr and HAPc-10%Sr are bioactive and can be potential candidates in bone tissue regeneration.</p>
Datapack for 'Nanocluster evolution and mechanical properties of ion irradiated T91 ferritic-martensitic steel' paper
<p>Data pack for the paper 'Nanocluster evolution and mechanical properties of ion irradiated T91 ferritic-martensitic steel', Journal of Nuclear Materials, 2021</p>
Lipid17ecc POPC:POPG 4:1 bilayer simulation in 1 M CaCl2 solution and Na+ counter ions
<p>Lipid17ecc POPC:POPG 4:1 bilayer simulation in 1 M CaCl2 solution. The initial structure was taken from https://zenodo.org/record/3874378#.X0OfthmEZGF . Temperature is 298 K. The system contains 350 POPC, 88 POPG, 88 Na+ ions, 24840 SPCE water molecules, 475 Ca2+ ions and 950 Cl- ions</p> <p>Total length of simulation is 400 ns. First 100 ns were discarded as equilibration time. Saving frequency of 100-300ns.xtc is 20 ps.</p>
Data from: Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing
The development and screening of microsatellite markers have been accelerated by next-generation sequencing (NGS) technology and in particular GS-FLX pyro-sequencing (454). More recent platforms such as the PGM semiconductor sequencer (Ion Torrent) offer potential benefits such as dramatic reductions in cost, but to date have not been well utilized. Here, we critically compare the advantages and disadvantages of microsatellite development using PGM semiconductor sequencing and GS-FLX pyro-sequencing for two gymnosperm (a conifer and a cycad) and one angiosperm species. We show that these NGS platforms differ in the quantity of returned sequence data, unique microsatellite data and primer design opportunities, mostly consistent with the differences in read length. The strength of the PGM lies in the large amount of data generated at a comparatively lower cost and time. The strength of GS-FLX lies in the return of longer average length sequences and therefore greater flexibility in producing markers with variable product length, due to longer flanking regions, which is ideal for capillary multiplexing. These differences need to be considered when choosing a NGS method for microsatellite discovery. However, the ongoing improvement in read lengths of the NGS platforms will reduce the disadvantage of the current short read lengths, particularly for the PGM platform, allowing greater flexibility in primer design coupled with the power of a larger number of sequences.
Data from: Dynamic pore structure evolution of the ion adsorbed rare earth ore during the ion exchange process
<p><span>During the leaching process of the ion adsorbed rare earth ore, the pore structure evolution of the ore body plays a vital role in the seepage of the leaching solution. To investigate the evolution of the pore structure during the leaching process, experiments have been carried out with remodeled rare earth ore samples based on physical characteristics of in-situ ores. The seepage rate difference between deionized water leaching solution and 2% NH<sub>4</sub>Cl leaching solution during the active leaching period are analyzed. The porosity and the dynamic pore size evolution of pore structures in the ore body are discussed. Results indicate that along with ion exchange between the rare earth ore and the leaching solution, the porosity of the sample remains constant and the pore structure shows a decreasing trend in the first part and an increasing trend in the second part. Specifically, during the ion exchange process, the number of minimal pores (0~5μm), small pores (5~10μm), and medium pores (10~25μm) increases significantly and the number of medium-large pores (25~60μm), large pores (60~120μm), and mega pores (>120μm) decreases dramatically. Along with the completion of the ion exchange process, the evolution of porous structure shows an opposite trend. The mechanism study reveals that the evolution of pore structure is induced by the difference of ionic strength in the leaching solution during the ion exchange process, where the rare earth ore microparticles will be absorbed or desorbed on to the solid phase.</span></p>
Data from: Probabilistic interfractional motion carbon ion radiation therapy dose distribution for prostate cancer shows rectum sparing with moderate target coverage degradation
Purpose: This observational study investigates the influence of interfractional motion on clinical target volume (CTV) coverage, planning target volume (PTV) margins, and rectum tissue sparing in carbon ion radiation therapy (CIRT). It reports dose coverage to target structures and organs at risk in the presence of interfractional motion, investigates rectal tissue sparing, and provides recommendations for further lowering the rate of toxicity. We also propose probabilistic DVH for consideration in treatment planning to represent probable dose to the clinic's patient population. Methods: At Gunma University Hospital intensity-modulated x-ray therapy (IMXT, aka IMRT) prostate cancer patients are positioned on a table which is shifted twice based on cone-beam computed tomography (CBCT) to align bones and then align prostate tissue to isocenter. These shifts thereby contain interfractional motion. 1306 such tableshifts from 85 patients were collected. Normal probability distributions were fit to the difference between bone-matching and prostate-matching CBCT-to-planning CT tableshifts (i.e. interfractional motion). Between 2011 and 2016 CIRT prostate patients were treated with PTV1 and PTV2 margins as follows: PTV1 extends the prostate contour by 10/10, 5/10, 6/6 mm in the right/left, posterior/anterior, and superior/inferior directions, respectively, and the proximal seminal vesicles contour by 5 mm superiorly and inferiorly, 3 mm right and left. PTV2 reduces PTV1 posteriorly along a straight line to exclude the rectum and reduces the superior and inferior margins by 6 mm. From those treated with these margins, 40 patients' beam data were selected to create probable interfractional motion: The previously fit normal probability distributions were randomly sampled 2000 times per patient and beams shifted to simulate this motion. These shifted dose distributions were scaled down proportionately in magnitude and summed to obtain probable blurred dose distributions. Results: Probable dose to rectum is substantially less than planned for doses higher than 10 Gy(RBE). Absolute DVH show that mean clinical target volumes are about 138-670 cm3 smaller for a given probable dose than planned doses higher than 57 Gy(RBE) after accounting for standard error. Cumulative DVH show mean CTV fraction receiving a given probable dose is less than the mean fraction receiving the corresponding planned dose for doses larger than 52 Gy(RBE), up to 19% less at 57.4 Gy(RBE). Our PTV1 margins generally cover 95% of interfractional motion but seminal vesicles and inferior prostate receive less dose than planned due to insufficient PTV2 margins. Conclusion: Assuming rigidly shifting interfractional motion around the prostate region and neglecting minor changes in soft tissue stopping power, interfractional motion resulted in underdosing or tissue sparing in all cases. Given our low rates of relapse and recurrence, it appears less curative dose is needed than previously thought or else the target may be smaller than previously thought. In-room CT may be useful to lower dose, shrink target margins, conduct PET auto-activation dose verification studies and account for interfractional motion.
Data from: Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity
The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology and lifestyle, tremendous diversity, paucity of formally described specimens, and the difficulty in isolating environmental strains into culture, fungal communities are difficult to characterize. This is especially true for endophytic communities of fungi living in healthy plant tissue. The developments in next generation sequencing technologies are, however, starting to reveal the true extent of fungal diversity. One of the promising new technologies, namely semiconductor sequencing, has thus far not been used in fungal diversity assessments. In this study we sequenced the internal transcribed spacer 1 (ITS1) nuclear encoded ribosomal RNA of the endophytic community of the economically important tree, Eucalyptus grandis, from South Africa using the Ion Torrent Personal Genome Machine (PGM). We determined the impact of various analysis parameters on the interpretation of the results, namely different sequence quality parameter settings, different sequence similarity cutoffs for clustering and filtering of databases for removal of sequences with insufficient taxonomy. Sequence similarity cutoff values only had a marginal effect on the identified family numbers, whereas different sequence quality filters had a large effect (89 vs. 48 families between least and most stringent filters). Database filtering had a small, but statistically significant, effect on the assignment of sequences to reference sequences. The community was dominated by Ascomycota, and particularly by families in the Dothidiomycetes that harbor well-known plant pathogens. The study demonstrates that semiconductor sequencing is an ideal strategy for environmental sequencing of fungal communities. It also highlights some potential pitfalls in subsequent data analyses when using a technology with relatively short read lengths.
Data from: Pumping ions: rapid parallel evolution of ionic regulation following habitat invasions
Marine to freshwater colonizations constitute among the most dramatic evolutionary transitions in the history of life. This study examined evolution of ionic regulation following saline-to-freshwater transitions in an invasive species. In recent years, the copepod Eurytemora affinis has invaded freshwater habitats multiple times independently. We found parallel evolutionary shifts in ion-motive enzyme activity (V-type H+ ATPase, Na+/K+-ATPase) across independent invasions and in replicate laboratory selection experiments. Freshwater populations exhibited increased V-type H+ ATPase activity in fresh water (0 PSU) and declines at higher salinity (15 PSU) relative to saline populations. This shift represented marked evolutionary increases in plasticity. In contrast, freshwater populations displayed reduced Na+/K+-ATPase activity across all salinities. Most notably, modifying salinity alone during laboratory selection experiments recapitulated the evolutionary shifts in V-type H+ ATPase activity observed in nature. Maternal and embryonic acclimation could not account for the observed shifts in enzyme activity. V-type H+ ATPase function has been hypothesized to be critical for freshwater and terrestrial adaptations, but evolution of this enzyme function had not been previously demonstrated in the context of habitat transitions. Moreover, the speed of these evolutionary shifts was remarkable, within a few generations in the laboratory and a few decades in the wild.
Data from: Erythrocyte stiffness during morphological remodeling induced by carbon ion radiation
The adverse effect induced by carbon ion radiation (CIR) is still an unavoidable hazard to the treatment object. Thus, evaluation of its adverse effects on the body is a critical problem with respect to radiation therapy. We aimed to investigate the change between the configuration and mechanical properties of erythrocytes induced by radiation and found differences in both the configuration and the mechanical properties with involving in morphological remodeling process. Syrian hamsters were subjected to whole-body irradiation with carbon ion beams (1, 2, 4, and 6 Gy) or X-rays (2, 4, 6, and 12 Gy) for 3, 14 and 28 days. Erythrocytes in peripheral blood and bone marrow were collected for cytomorphological analysis. The mechanical properties of the erythrocytes were determined using atomic force microscopy, and the expression of the cytoskeletal protein spectrin-α1 was analyzed via western blotting. The results showed that dynamic changes were evident in erythrocytes exposed to different doses of carbon ion beams compared with X-rays and the control (0 Gy). The magnitude of impairment of the cell number and cellular morphology manifested the subtle variation according to the irradiation dose. In particular, the differences in the size, shape and mechanical properties of the erythrocytes were well exhibited. Furthermore, immunoblot data showed that the expression of the cytoskeletal protein spectrin-α1 was changed after irradiation, and there was a common pattern among its substantive characteristics in the irradiated group. Based on these findings, the present study concluded that CIR could induce a change in mechanical properties during morphological remodeling of erythrocytes. According to the unique characteristics of the biomechanical categories, we deduce that changes in cytomorphology and mechanical properties can be measured to evaluate the adverse effects generated by tumor radiotherapy. Additionally, for the first time, the current study provides a new strategy for enhancing the assessment of the curative effects and safety of clinical radiotherapy, as well as reducing adverse effects.
MD simulation trajectory and related files for POPC bilayer with 340mM NaCl (Berger model delivered by Tieleman, ffgmx ions, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Berger force field delivered by Peter Tieleman (http://wcm.ucalgary.ca/tieleman/downloads), double bonds updated in http://dx.doi.org/10.1021/jp065424f, ffgmx parameters for ions, 50ns, T=298K, 128 POPC molecules, 7202 water molecules, 44 Na molecules, 44 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi).</p>
MD simulation trajectory and related files for POPC bilayer with 340mM CaCl_2 (Berger model delivered by Tieleman, ffgmx ions, Gromacs 4.5)
<p>Equilibrated POPC lipid bilayer simulation ran with Gromacs 4.5, Berger force field delivered by Peter Tieleman (http://wcm.ucalgary.ca/tieleman/downloads) double bonds updated in http://dx.doi.org/10.1021/jp065424f, ffgmx parameters for ions, 50ns, T=298K, 128 POPC molecules, 7157 water molecules, 44 Na molecules, 88 Cl molecules. This data is used in the NMRLipids II project (nmrlipids.blospot.fi).</p>
Partial density profiles of lipids and ions
<p>Partial density profiles of lipids and ions calculated using the script available on Zenodo. Each simulated system contains 600 DPPC molecules, 150 mM NaCl and 30 waters/lipid. The ion model is the one described by Roux. The analysis has been performed over the last 40 ns of each 100 ns trajectory. All simulations have been performed with the Slipids force field.</p>
POPC @ 310K, 450 mM of CaCl_2. Charmm36 with ECC-scaled ions
<p>Simulations of a POPC bilayer with 450 mM of CaCl_2. <br> The goal was to study the effect of salt on the order <br> parameters of the lipid head group and the glycerol <br> backbone for the NMRlipids project, see <br> http://nmrlipids.blogspot.fi for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 450 mM CaCl_2. The Charmm36 <br> model is employed for lipids, the Charmm compatible variant <br> of the tip3p model for water, and the recent ion parameters <br> by Kohagen et al. [2] for CaCl_2.</p> <p>The Charmm36 force field parameters were obtained from<br> CHARMM-GUI [3] at http://www.charmm-gui.org</p> <p>The ion parameters are available at<br> https://bitbucket.org/hseara/ions/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. These data<br> were collected once the adsorption and desorption of <br> CaCl_2 to the surface has reached equilibrium, namely<br> after 700 ns of simulation. Additionally, the initial <br> structure (.gro), topology (.top), index file (.ndx), <br> simulation paremeter file (.mdp), binary run input file <br> for GROMACS v. 5.0–> (.tpr) and the energy output file <br> (.edr) are provided. </p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Update of the CHARMM All-Atom Additive Force Field <br> for Lipids: Validation on Six Lipid Types<br> Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, <br> Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, <br> Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor<br> The Journal of Physical Chemistry B 2010 114 (23), 7830-7843<br> DOI: 10.1021/jp101759q</p> <p>[2] Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions<br> Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth<br> The Journal of Physical Chemistry B 2014 118 (28), 7902-7909<br> DOI: 10.1021/jp5005693</p> <p>[3] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, <br> and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field<br> Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, <br> Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, <br> Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, <br> Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im<br> Journal of Chemical Theory and Computation 2016 12 (1), 405-413<br> DOI: 10.1021/acs.jctc.5b00935</p>
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.