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opencc-zeroDec 2012View details →

Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals' diet. Seals were fed fish in fixed proportions, a chordate-specific mitochondrial 16S marker was amplified from scat DNA and amplicons sequenced using an Ion Torrent PGM™. For a given set of bioinformatic parameters, there was generally low variability between scat samples in proportions of prey species sequences recovered. However, proportions varied substantially depending on sequencing direction, level of quality filtering (due to differences in sequence quality between species) and minimum read length considered. Short primer tags used to identify individual samples also influenced species proportions. In addition, there were complex interactions between factors; for example, the effect of quality filtering was influenced by the primer tag and sequencing direction. Resequencing of a subset of samples revealed some, but not all, biases were consistent between runs. Less stringent data filtering (based on quality scores or read length) generally produced more consistent proportional data, but overall proportions of sequences were very different than dietary mass proportions, indicating additional technical or biological biases are present. Our findings highlight that quantitative interpretations of sequence proportions generated via high-throughput sequencing will require careful experimental design and thoughtful data analysis.

opencc-zeroDec 2014View details →

Data from: Convergence of ion channel genome content in early animal evolution

Multicellularity has evolved multiple times, but animals are the only multicellular lineage with nervous systems. This fact implies that the origin of nervous systems was an unlikely event, yet recent comparisons among extant taxa suggest that animal nervous systems may have evolved multiple times independently. Here, we use ancestral gene content reconstruction to track the timing of gene family expansions for the major families of ion-channel proteins that drive nervous system function. We find that animals with nervous systems have broadly similar complements of ion-channel types but that these complements likely evolved independently. We also find that ion-channel gene family evolution has included large loss events, two of which were immediately followed by rounds of duplication. Ctenophores, cnidarians, and bilaterians underwent independent bouts of gene expansion in channel families involved in synaptic transmission and action potential shaping. We suggest that expansions of these family types may represent a genomic signature of expanding nervous system complexity. Ancestral nodes in which nervous systems are currently hypothesized to have originated did not experience large expansions, making it difficult to distinguish among competing hypotheses of nervous system origins and suggesting that the origin of nerves was not attended by an immediate burst of complexity. Rather, the evolution of nervous system complexity appears to resemble a slow fuse in stem animals followed by many independent bouts of gene gain and loss.

Data from: Fast formation of a supramolecular ion gel/solvoplastic elastomer with excellent stretchability

This study describes a simple yet efficient approach for the preparation of an ionic gel that is also elastomeric in its solid state bulk form. A series of poly(2-(Diethylamino)ethyl methacrylate-co-Lauryl methacrylate) P(DMAEMA-co-LMA) copolymer were synthesized first by radical polymerization. Quaternization of the PDMAEMA component in THF enables the formation of supramolecular network, gave rise to an ion gel. An elastomer with an elongation at break of over 600 % was obtained from the gel. The elastomer, connected by supramolecular ionic crosslinks, is solvoplastic in certain solvent. The simple yet efficient approach of the formation of ion-gel and the dried elastomer allows fast preparation of both gel-like and solid-state elastic materials for various applications where recyclability are required.

opencc-zeroDec 2016View details →

Data from: Chromium oxide coatings with the potential for eliminating the risk of chromium ion release in orthopaedic implants

Chromium oxide coatings prepared by radiofrequency reactive magnetron sputtering on stainless steel substrates were exposed to Ringer's physiological solution and tested for their electrochemical corrosion stability using an open circuit potential measurement, potentiodynamic polarization, electrochemical impedance spectroscopy and Mott–Schottky analysis. The coatings were found to be predominantly Cr2O3, based on the observation of the dominance of A1gA1g and Eg symmetric modes in our Raman spectroscopic investigation and the Eu vibrational modes in our Fourier transform infrared spectroscopic measurements on the coatings. We investigated for the presence of chromium ions in Ringer's solution after all of the above electrochemical tests using atomic absorption spectroscopy, without finding a trace of chromium ions at the ppm level for coatings tested under open circuit and at the lower potentials implants are likely to experience in the human body. The coatings were further exposed to Ringer's solution for one month and tested for adhesion strength changes, and we found that they retained substantial adhesion to the substrates. We expect this finding to be significant for future orthopaedic implants where chromium ion release is still a major challenge.

Data from: Removal of Cr6+ ions from water by electricosorption on modified activated carbon fibre felt

Electrosorption is a novel desalination technique that has many advantages in the treatment of sewage. However, commercially available activated carbon electrodes for electrosorption commonly have low microporosity, poor molding performance, and low adsorption and regeneration efficiency. Here we evaluated a novel adsorbent material, activated carbon fiber felt (ACFF), for electrosorption of chromium ions (Cr6+) in sewage treatment. The ACFF was modified with 20% nitric acid and its modified structure was characterized. The modified ACFF was used as an adsorbing electrode to investigate its desalination effect by electrosorption. Results showed that compared with those of unmodified ACFF, the modified ACFF had more carbonyl and carboxyl groups and the specific surface area, average pore size and micropore volume of the modified ACFF also improved by 32.2%, 2.5%, and 23.1%, respectively. The kinetics of Cr6+ adsorption conformed to the pseudo-second order kinetic equation, and the adsorption isotherm conformed to the Langmuir model. In addition, the regeneration rate of the modified ACFF electrode was more than 94%. In conclusion, the modified ACFF exhibits excellent electrosorption and regeneration performance for Cr6+ removal from water and thus is of great value for promotion in sewage treatment.

Data from: Electrochemical performance of ZnO-coated Li4Ti5O12 composite electrodes for lithium-ion batteries with the voltage ranging from 3 to 0.01 V

Oxide is widely used in modifying cathode and anode materials for lithium ion batteries. In this work, a facial method of radio magnetron sputtering is introduced to deposit a thin film on Li4Ti5O12 composite electrodes. The pristine and modified Li4Ti5O12 electrodes are characterized at an extended voltage range of 3-0.01 V. The reversible capacity reach a high level of 286 mAh g-1, which is a little less than its theoretical capacity (293 mAh g-1). Electrodes modified by ZnO thin films with various thickness show elevated rate capability and improved cycle performance.

opencc-zeroDec 2016View details →

Data from: Electrospinning preparation of oxygen-deficient nano TiO2-x/carbon fibre membrane as a self-standing high performance anode for Li-ion batteries

Improving the specific capacity and electronic conductivity of TiO2 can boost its practical application as a promising anode material for lithium ion batteries. In this work, a three-dimensional networking oxygen-deficient nano TiO2-x/carbon fibre membrane was achieved by combining the electrospinning process with a hot-press sintering method and directly used as a self-standing anode. With the synergistic effects of three-dimensional conductive networks, surface oxygen deficiency, high specific surface area and high porosity, binder-free and self-standing structure, etc., the nano TiO2-x/carbon fibre membrane electrode displays a high electrochemical reaction kinetics and a high specific capacity. The reversible capacity could be jointly generated from porous carbon, full-lithiation of TiO2 and interfacial lithium storage. At a current density of 100 mA g−1, the reversible discharge capacity can reach 464 mA h g−1. Even at 500 mA g−1, the discharge capacity still remains at 312 mA h g−1. Compared with pure carbon fibre and TiO2 powder, the TiO2-x/C fibre membrane electrode also exhibits an excellent cycle performance with a discharge capacity of 209 mA h g−1 after 700 cycles at the current density of 300 mA g−1, and the coulombic efficiency always remains at approximately 100%.

opencc-zeroDec 2018View details →

Data from: Preparation of modified pomelo peel's pulp adsorbent and its adsorption to uranyl ions

Using Pomelo peel's pulp (PPP) as raw materials, the new chemically modified PPP was prepared by the process of fermentation, cooking, freeze-drying, and so on. The adsorbent were characterized by SEM, IR, BET and EDS. The effects of different adsorption conditions such as pH value, adsorption temperature, mass of adsorbent, adsorption time, and initial concentration of UO22+ were studied. The adsorption mechanism was explored through adsorption thermodynamics and adsorption kinetics experiments. The results show that the pH value is 6.0, the dosage of adsorbent is 10 mg, the temperature is 50℃ and the adsorption time is 90 min, which is the best adsorption condition. When the initial concentration of UO22+ is 35 mg/L, the adsorbed capacity of uranyl ion by the modified PPP adsorbent can reach 42.733 mg/g, 26.8% higher than the adsorption capacity of unmodified adsorbent (31.276 mg/g), which is obviously enhanced. The kinetic and thermodynamic experiments show that the adsorption process accords with the pseudo-second-order kinetics model and is an endothermic reaction, and the reaction is spontaneous. The adsorption process is dominated by entropic. The Freundlich adsorption isotherm can describe the adsorption process more accurately.

Data from: Screening of candidate substrates and coupling ions of transporters by thermostability shift assays

Substrates of most transport proteins have not been identified, limiting our understanding of their role in physiology and disease. Traditional identification methods use transport assays with radioactive compounds, but they are technically challenging and many compounds are unavailable in radioactive form or are prohibitively expensive, precluding large-scale trials. Here, we present a high-throughput screening method that can identify candidate substrates from libraries of unlabeled compounds. The assay is based on the principle that transport proteins recognize substrates through specific interactions, which lead to enhanced stabilization of the transporter population in thermostability shift assays. Representatives of three different transporter (super)families were tested, which differ in structure as well as transport and ion coupling mechanisms. In each case, the substrates were identified correctly from a large set of chemically related compounds, including stereo-isoforms. In some cases, stabilization by substrate binding was enhanced further by ions, providing testable hypotheses on energy coupling mechanisms.

opencc-zeroDec 2015View details →

POPC @ 310K, varying amounts of NaCl. Slipids with ECC-scaled ions

Simulations of a POPC bilayer with varying amounts of NaCl. These simulations were performed as a part of the NMRlipids project (http://nmrlipids.blogspot.fi). The goal was to study  the effect of salt on the order parameters of the lipid head  group and the glycerol backbone. The obtained results are  reported in the blog. A POPC bilayer consisting of 200 lipids (100 per leaflet) is  simulated in the presence of NaCl. Concentrations of 130, 300,  500, 750, and 1000 mM are employed. The Slipids model [1–3] is  employed for lipids, tip3p model for water, and the recent ion  parameters by Kohagen et al. [4] for NaCl.  The Slipids force field parameters were downloaded from http://mmkluster.fos.su.se/slipids/ The ion parameters are available at https://bitbucket.org/hseara/ions/ –––––––––––––––––––––––––––––––––––––––––––––––––––––– The files are named based on the concentration of NaCl and are in GROMACS format. Trajectories (.xtc) are  100 ns long with data saved every 100 ps. Additionally, initial structures (.gro), topology (.top), index (.ndx) and binary run input files for GROMACS v. 4.6–> (.tpr) are provided. The run parameter file (.mdp) is general for all systems. –––––––––––––––––––––––––––––––––––––––––––––––––––––– [1] Derivation and Systematic Validation of a Refined  All-Atom Force Field for Phosphatidylcholine Lipids Joakim P. M. Jämbeck and Alexander P. Lyubartsev The Journal of Physical Chemistry B 2012 116 (10), 3164-3179 DOI: 10.1021/jp212503e   [2] An Extension and Further Validation of an All-Atomistic  Force Field for Biological Membranes Joakim P. M. Jämbeck and Alexander P. Lyubartsev Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948 DOI: 10.1021/ct300342n   [3] Another Piece of the Membrane Puzzle: Extending Slipids Further Joakim P. M. Jämbeck and Alexander P. Lyubartsev Journal of Chemical Theory and Computation 2013 9 (1), 774-784 DOI: 10.1021/ct300777p   [4] Accounting for Electronic Polarization Effects in Aqueous Sodium  Chloride via Molecular Dynamics Aided by Neutron Scattering Miriam Kohagen, Philip E. Mason, and Pavel Jungwirth The Journal of Physical Chemistry B Article ASAP DOI: 10.1021/acs.jpcb.5b0522

opencc-by-sa-4.0Sep 2016View details →

CO-2 capture using alkali earth ions: an effect of the non-coordinating anion.

100ps MD trajectories for 8 systems Mg Ca Sr Ba Mg + TFPB Ca + TFPB Sr + TFPB Ba + TFPB

opencc-zeroNov 2023View details →

Supplementary material 1 from: Satmari A, Miok K, Ion MC, Zaharia C, Schrimpf A, Pârvulescu L (2023) Headwater refuges: Flow protects Austropotamobius crayfish from Faxonius limosus invasion. NeoBiota 89: 71-94. https://doi.org/10.3897/neobiota.89.110085

Hyperparameter tuning using Grid Search

opencc-by-4.0Jul 2023View details →

The response of silicon carbide composites to He ion implantation and ramifications for use as a fusion reactor structural material

Raw and processed datasets for the publication "The response of silicon carbide composites to He ion implantation and ramifications for use as a fusion reactor structural material".

Caribbean Regional Annual Hard Coral Coverage (%) with Regional Annual Surface Ocean Hydrogen Ion Activity (10^-9 mol/kg)

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openDec 2023View details →

High accuracy QM data for dimers of water with self, Cl- ion, Na+ ion, Li+ ion, acetate ion, acetamide, and n-methylacetamide

The dataset is the large dataset of quantum-mechanically calculated dimers. QM calculated dimers of water with itself, Cl- ion, Na+ ion, Li+ ion, acetate ion, acetamide, n-methyl-acetamide. This is a subset of dimers that has been used in the published work: <a href="https://doi.org/10.1021/jacs.3c07628">https://doi.org/10.1021/jacs.3c07628</a> . Total count of all the dimers is around 535 thousand configurations. The dimer energetics were calculated with silver standard and using counter-poise correction. The silver standard is MP2/CBS energies calculated and by extrapolating MP2/aug-cc-pvtz->MP2/aug-cc-pvqz + post-mp2 correction CCSD(T)/aug-cc-pvdz-MP2/aug-cc-pvdz. The configurations of dimers are presented in .hin format. Description of the hin format is here (https://wiki.jmol.org/index.php/File_formats/Formats/HIN). All coordinates in the hin files are in the angstrom units. Each hin file has two comment tags that describe energies of this configurations: 1) ";conf-ccmp2-EnergyDimer(KCAL/MOL)" - which is the total silver standard energy in kcal/mol units 2) ";conf-CCSDt-mp2-correction-added-to-EN-and-DS(KCAL/MOL)" - which is the post-mp2 correction =CCSD(T)/aug-cc-pvdz-MP2/aug-cc-pvdz

East Asian Sea Regional Annual Hard Coral Coverage (%) with Regional Annual Surface Ocean Hydrogen Ion Activity (10^-9 mol/kg)

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Gulf of Oman Regional Annual Hard Coral Coverage (%) with Regional Annual Surface Ocean Hydrogen Ion Activity (10^-9 mol/kg)

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Pacific Regional Annual Hard Coral Coverage (%) with Regional Annual Surface Ocean Hydrogen Ion Activity (10^-9 mol/kg)

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South Asia Regional Annual Hard Coral Coverage (%) with Regional Annual Surface Ocean Hydrogen Ion Activity (10^-9 mol/kg)

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