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CD226 is an activating receptor expressed on the cell surface of natural killer cells and T cells. Although CD226 polymorphism is known to be involved in systemic lupus erythematosus (SLE), the involvement of soluble CD226 (sCD226) in SLE is still unknown. In the present study, we measured serum sCD226 levels using an enzyme-linked immunosorbent assay in 58 SLE patients and 33 healthy controls (HCs) and evaluated their associations with SLE Disease Activity Index 2000 (SLEDAI-2K), clinical manifestations, laboratory data, and the cumulative probability of flare. Serum sCD226 levels showed no significant differences between SLE patients and HCs. However, sCD226 levels were significantly elevated in active SLE patients with a SLEDAI-2K score of ≥ 20 compared with HCs. In SLE patients, sCD226 levels were significantly correlated with SLEDAI-2K scores and anti-dsDNA antibody titers. Moreover, the cumulative probability of flare was markedly higher in patients with high sCD226 than in those with low sCD226. In patients with neuropsychiatric involvement, sCD226 levels were elevated and reflected neuropsychiatric disease activity. These findings indicate that serum sCD226 levels are associated with disease activity and flares of SLE. Thus, it may be a useful biomarker for SLE, and its monitoring allows for more precise SLE management. [ABSTRACT FROM AUTHOR]

Three‐dimensional (3D) structures of biomolecules provide insight into their functions. Using X‐ray free‐electron laser (XFEL) scattering experiments, it was possible to observe biomolecules that are difficult to crystallize, under conditions that are similar to their natural environment. However, resolving 3D structure from XFEL data is not without its challenges. For example, strong beam intensity is required to obtain sufficient diffraction signal and the beam incidence angles to the molecule need to be estimated for diffraction patterns with significant noise. Therefore, it is important to quantitatively assess how the experimental conditions such as the amount of data and their quality affect the expected resolution of the resulting 3D models. In this study, as an example, the restoration of 3D structure of ribosome from two‐dimensional diffraction patterns created by simulation is shown. Tests are performed using the diffraction patterns simulated for different beam intensities and using different numbers of these patterns. Guidelines for selecting parameters for slice‐matching 3D reconstruction procedures are established. Also, the minimum requirements for XFEL experimental conditions to obtain diffraction patterns for reconstructing molecular structures to a high‐resolution of a few nanometers are discussed. [ABSTRACT FROM AUTHOR]

The three-dimensional (3D) structural analysis of single particles using an X-ray free-electron laser (XFEL) is a new structural biology technique that enables observations of molecules that are difficult to crystallize, such as flexible biomolecular complexes and living tissue in the state close to physiological conditions. In order to restore the 3D structure from the diffraction patterns obtained by the XFEL, computational algorithms are necessary as the orientation of the incident beam with respect to the sample needs to be estimated. A program package for XFEL single-particle analysis based on the Xmipp software package, that is commonly used for image processing in 3D cryo-electron microscopy, has been developed. The reconstruction program has been tested using diffraction patterns of an aerosol nanoparticle obtained by tomographic coherent X-ray diffraction microscopy. [ABSTRACT FROM AUTHOR]

Thermodynamic properties of water molecules around single- and double-stranded DNAs (ssDNAs and dsDNAs) with different sequences were investigated using grid inhomogeneous solvation theory. Free energies of water molecules solvating the minor groove of dsDNAs are lower than those near ssDNAs, while water molecules should be released during the formation of dsDNA. Free energies of water molecules around dsDNA are lower than those around ssDNA even in the second and third hydration shells. Our findings will help to clarify the role of water molecules in the formation of dsDNA from ssDNAs, thus facilitating the designs of drugs or nanomaterials using DNA. [ABSTRACT FROM AUTHOR]

Thermodynamic analyses and molecular dynamics calculations demonstrated that i-motifs in a hydrated ionic liquid of choline dihydrogen phosphate (choline dhp) were more stable than G-quadruplexes due to choline ion binding to loop regions in the i-motifs. Interestingly, the i-motifs formed even at physiological pH in the choline dhp-containing solution. [ABSTRACT FROM AUTHOR]

Itis considered that Hoogsteen base pairs and DNA triplex structuresplay important roles in cellular processes even though these structuresare less than duplexes of Watson–Crick base pairs. Molecularions clearly affect the stability of DNA structures in vivo; however,the mechanisms are unknown. Here, we investigated the effects of sodiumions, choline ions, and tetramethylammonium ions on DNA triplexesusing molecular dynamics simulations. We found that nonpolar interactions,which are associated with van der Waals interactions, and solvent-accessiblesurface area were more important than polar or electrostatic interactionsin determining the affinity of a molecular cation for the DNA grooveareas. The free energy gain due to a cation that fit optimally withina DNA groove was larger than the free energy loss due to the effectof dehydration. Cations with shapes complementary to that of a particularDNA groove configuration stabilized triplex formation, but cationsthat disturbed hydrogen bonds between DNA bases were destabilizing.These stabilizing and destabilizing mechanisms of molecular cationswere also applicable to a DNA duplex composed of Watson–Crickbase pairs. The molecular-level view of cation interactions with DNAstructures will guide the design of DNA devices, DNA-based drugs,and genetic therapies. [ABSTRACT FROM AUTHOR]

Highlights: [•] Classical density functional theory for liquid water is formulated. [•] Triplet correlations and bridge functions are taken into account. [•] Factorization approximation for ternary direct correlation functions is employed. [•] Radial distribution functions for liquid water are calculated and compared with simulation results. [ABSTRACT FROM AUTHOR]

Underphysiological conditions, G–C base pairs are morestable than A–T base pairs. In a previous study, we showedthat in the hydrated ionic liquid of choline dihydrogen phosphate,the stabilities of these base pairs are reversed. In the present study,we elucidated the unique binding interactions of choline ions withDNA atoms from a microscopic viewpoint using molecular dynamics simulations.Three times more choline ions bind to the DNA duplex than sodium ions.Sodium ions bind closely but not stably; in contrast, the cholineions bind through multiple hydrogen bonding networks with DNA atomsstably. The affinity of choline ion for the minor groove of A–Tbase pairs is more than 2 times that for other groove areas. In thenarrow A–T minor groove, choline ion has high affinity forthe ribose atoms of thymine. Choline ions also destabilize the formationof hydrogen bonds between G–C base pairs by binding to baseatoms preferentially for both of duplex and single-strand DNA, whichare associated with the bonds between G–C base pairs. Our newfinding will not only lead to better control of DNA stability foruse in DNA nanodevices, but also provide new insight into the stabilityof DNA duplexes under crowding conditions found in living cells. [ABSTRACT FROM AUTHOR]

The instability of Hoogsteen base pairs relative to Watson-Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson- Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson-Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo. [ABSTRACT FROM AUTHOR]

Highlights: [•] A classical density functional theory for molecular liquids is formulated. [•] Triplet correlations and associated bridge functions are taken into account. [•] A factorization ansatz for the triplet direct correlation functions is employed. [•] Radial distribution functions for liquid water are calculated and compared with simulation results. [Copyright &y& Elsevier]

Polyglutamine (polyQ, a peptide) with an abnormal repeat length is the causative agent of polyQ diseases, such as Huntington's disease. Although glutamine is a polar residue, polyQ peptides form insoluble aggregates in water, and the mechanism for this aggregation is still unclear. To elucidate the detailed mechanism for the nucleation and aggregation of polyQ peptides, replica exchange molecular dynamics simulations were performed for monomers and dimers of polyQ peptides with several chain lengths. Furthermore, to determine how the aggregation mechanism of polyQ differs from those of other peptides, we compared the results for polyQ with those of polyasparagine and polyleucine. The energy barrier between the monomeric and dimeric states of polyQ was found to be relatively low, and it was observed that polyQ dimers strongly favor the formation of antiparallel β-sheet structures. We also found a characteristic behavior of the monomeric polyQ peptide: a turn at the eighth residue is always present, even when the chain length is varied. We previously showed that a structure including more than two sets of β-turns is stable, so a long monomeric polyQ chain can act as an aggregation nucleus by forming several pairs of antiparallel β-sheet structures within a single chain. Since the aggregation of polyQ peptides has some features in common with an amyloid fibril, our results shed light on the mechanism for the aggregation of polyQ peptides as well as the mechanism for the formation of general amyloid fibrils, which cause the onset of amyloid diseases. [ABSTRACT FROM AUTHOR]

Polyglutamine (polyQ) diseases are caused by an abnormal expansion of CAG repeats. While their detailed structure remains unclear, polyQ peptides assume β-sheet structures when they aggregate. To investigate the conformational ensemble of short, monomeric polyQ peptides, which consist of 15 glutamine residues (Q15), we performed replica exchange molecular dynamics (REMD) simulations. We found that Q15 can assume multiple configurations due to all of the residues affecting the formation of side-chain hydrogen bonds. Analysis of the free energy landscape reveals that Q15 has a basin for random-coil structures and another for α-helix or β-turn structures. To investigate properties of aggregated polyQ peptides, we performed multiple molecular dynamics (MMD) simulations for monomeric and oligomeric Q15. MMD revealed that the formation of oligomers stabilizes the β-turn structure by increasing the number of hydrogen bonds between the main chains. [ABSTRACT FROM AUTHOR]

Abstract: We perform potential energy calculations on mutant polyglutamine peptides that were studied experimentally, and found to aggregate with varying efficiencies. Low-energy structures were generated for each peptide by simulated annealing molecular dynamics, and were analyzed by molecular mechanics and by all-electron fragment molecular orbital energy calculations. In order to make a comparison between the two sets of potential energies, we devised a means of computing molecular-mechanical analogues of the quantum-mechanical energies. Our results suggest that in accordance with a previous paper (VanSchouwen et al., submitted for publication ) the experimentally-observed inhibition of aggregation is due to localized, geometry-based effects on peptide structure, with little appreciable perturbation from longer-range non-bonded effects. [Copyright &y& Elsevier]

Abstract: The frictional properties of self-assembled monolayers (SAMs) covalently bonded to silicon (Si) substrates through Si–C or Si–O–C bonds were investigated using a pin-on-plate tribometer. Four kinds of molecules with different alkyl chain lengths and different head groups were used: 1-hexadecene, 1-hexadecanol, 1-dodecene and 1-dodecanol. The SAMs with longer alkyl chains exhibited lower friction coefficients than those with shorter alkyl chains. Of the SAMs with longer alkyl chains, the SAMs with the Si–C bond of the head group exhibited lower friction coefficients, higher wear resistance and higher durability than those with the Si–O–C bond. The head group and alkyl chain length of the molecules affected the frictional properties of the modified surfaces of the SAMs. [Copyright &y& Elsevier]

Abstract: It is known that Huntington''s disease patients commonly have glutamine (Q) repeat sequences longer than a critical length in the coding area of Huntingtin protein in their genes. As the polyglutamine (polyQ) region becomes longer than the critical length, the disease occurs and Huntingtin protein aggregates, both in vitro and in vivo, as suggested by experimental and clinical data. The determination of polyglutamine structure is thus very important for elucidation of the aggregation and disease mechanisms. Here, we perform molecular dynamics calculations on the stability of the structure based on the β-helix structure suggested by Perutz et al. (2002) [Perutz, M.F., Finch, J.T., Berriman, J., Lesk, A., 2002. Amyloid fibers are water-filled nanotubes. Proc. Natl. Acad. Sci. USA 99, 5591]. We ensure that perfect hydrogen bonds are present between main chains of the β-helix based on the previous studies, and perform simulations of stretches with 20, 25, 30, 37 and 40 glutamine residues (20Q, 25Q, 30Q, 37Q and 40Q) for the Perutz models with 18.5 and 20 residues per turn (one coil). Our results indicate that the structure becomes more stable with the increase of repeated number of Q, and there is a critical Q number of around 30, above which the structure of the Perutz model is kept stable. In contrast to previous studies, we started molecular dynamics simulations from conformations in which the hydrogen bonds are firmly formed between stacked main chains. This has rendered the initial β-helix structures of polyQ much more stable for longer time, as compared to those proposed previously. Model calculations for the initial structures of polyQ dimer and tetramer have also been carried out to study a possible mechanism for aggregation. [Copyright &y& Elsevier]

Abstract: We investigated the frictional properties and the durability of self-assembled double layers using pin-on-plate methods and X-ray photoelectron spectroscopy (XPS). We found that double layers made from octadecanethiol (ODT) and mercaptohexadecanoic acid (MHA) connected via Cu ions exhibited lower frictional coefficients (approximately 0.1–0.15) than that of ODT monolayer (∼0.2). XPS measurements revealed that ratios of C(1s)/Au(4f) after friction tests were lower than that before friction but was higher than that measured on ODT monolayer, suggesting that some of ODT molecules were desorbed from the surface, i.e. formation of loosely packing molecular layers after friction. These findings suggest that the loosely packed molecular layer contributed to decrease the friction. [Copyright &y& Elsevier]

[Display omitted] • Cephalopod-inspired extremely rapid self-repairing coatings are designed that can repair surface. • The introduction of counter-ions into polyelectrolyte multilayers produces the mimicking coatings. • Mimicking the cephalopod's self-healing mechanisms achieved ultrafast self-repair within 10 sec. • The key technology has various potential applications and contributes to the development of a sustainable society. Emerging materials capable of self-repair to damaged areas are attracting attention for environmental protection and energy reduction. Although coatings whose material elasticity physically restores surface-dents are in practical use, in the case of crack damage, they cannot perform their self-repairing function. Conversely, coatings that exhibit the capacity to repeatedly repair themselves chemically have been challenged by long repair times. Here water-induced, self-repairing coatings inspired by cephalopod self-healing mechanisms were developed that can ultra-rapidly repair surface scratches. The introduction of counter-ions into polyelectrolyte multilayers produced coatings mimicking the strong β -sheet structures, noncovalent intermolecular interactions, and consequently self-repair process in cephalopods. These features resulted in a decrease in the strong polycation–polyanion electrostatic bonds and an increase in the noncovalent polymer networks. Furthermore, counter-ion addition improved the coating's water absorption and retention properties. The ion-trapped polymer networks facilitated expansion in the horizontal direction where a scar was present, resulting in ultrafast self-repairing rate of 92% in 1 s and 100% in 10 s. These extremely rapidly self-repairing coatings have various potential applications given knowledge acceleration via machine learning. The key technology developed here paves the way for novel insights into the construction of self-repairing materials and contributes to the development of a sustainable society. [ABSTRACT FROM AUTHOR]

A correction to the article "Comparative Characterization of Short Monomeric Polyglutamine Peptides by Replica Exchange Molecular Dynamics Simulation," published in a 2010 issue is presented.

The molecular behavior of room-temperature ionic liquids (RTILs) under lubricating condition was analyzed using fourier transform infrared spectroscopy equipped with a pin-on-disk tribometer to simultaneously measure the friction force, normal load, and IR spectrum. When 1-metyl-3-butylimidazolium trifluoromethanesulfonate ([BMIM]OTf), which is miscible with water, was used as a lubricant, the water content increased with time, and the ratio of water to cation remained constant even though the film thickness reduced under the lubricating condition at a load of ~25 N. When 1-metyl-3-butylimidazolium tetrafluorophosphate ([BMIM]PF), which is water-insoluble, was used as a lubricant, the water content was quite small and increased slightly with time, and the ratio of water to cation also remained constant even when a normal load of ~25 N was applied. The SUJ2 pin surface showed oxidative discoloration after the friction test using [BMIM]OTf, but there was little change in color when[BMIM]PF was used. XPS results indicated that iron oxide, chromium oxide and sulfate were observed on the worn pin surface using [BMIM]OTf and the CaF disk. However, iron oxide and iron phosphate were observed for the worn pin surface using [BMIM]PF and the CaF disk. These results suggest that the amount of water contained in the RTILs as well as window materials have a significant effect on the tribo-chemical reaction of RTILs. [ABSTRACT FROM AUTHOR]

Objective: To determine the success rate and complications of using the external jugular vein (EJV) for central venous access with a preoperative estimate of the detailed anatomical orientation of the cervical venous plexus using computed tomography venography (CT-V). Design: Prospective, observational human study. Setting: Surgical intensive care unit. Patients: Fifty-two patients who were undergoing EJV cannulations with CT-V using a Multidetector Helical 16-section CT (MDCT). Intervention: The preoperative anatomical estimation of the cervical venous plexus was performed with CT-V using an MDCT. In particular, the angulation between the EJV and the right subclavian vein (SCV) was measured. The anatomical abnormalities and the angulation between the EJV and the anterior jugular vein (AJV), transverse cervical vein (TCV), and suprascapular vein (SSV) were estimated. Measurements and Main Results: The success of CT-V was achieved in 52 of 52 patients (100%). The mean angulation between the right EJV and the right SCV was 144 ± 36 degrees in the obtuse-angle cases (88%) and 72 ± 28 degrees in the sharp-angle cases (12%). A plexus of veins under the clavicle was most commonly responsible for insertion of the central venous catheter (CVC). The EJV approach resulted in a 93% rate of successful cannulations. No complications of pneumothorax or carotid artery puncture occurred during insertion procedures. Conclusions: The EJV route is associated with comparable technical success and lower major procedural complication. The EJV approach with CT-V guidance is an option as the initial method when central venous cannulation must be performed under suboptimal conditions. [ABSTRACT FROM AUTHOR]

Ionic liquids are expected to be used as new high-performance lubricants because of their low volatility, high thermal stability, and high oxidation stability. It is well known that halogen-containing ionic liquids exhibit excellent lubricity for metals. However, there is a concern about the corrosiveness of ionic liquids caused by the formation of halides. The lubricity of halogen-free ionic liquids for metals is inferior to that of halogen-containing ionic liquids; however, they do not cause any remarkable corrosion effects. In this study, the lubricity of halogen-free ionic liquids-1-butyl-3-methylimidazolium tricyanomethanide ([BMIM] [TCC]) and 1-ethyl-3-methylimidazolium dicyanamide ([EMIM] [DCN])-for hard coatings and ceramics was evaluated using an SRV oscillating sliding tester. Ionic liquids exhibited excellent lubricity for sintered ceramics. It is supposed that the lubricity of ceramics depends on the chemical interaction between the surface and the ionic liquids. Ionic liquids exhibited different lubricating properties with each nitride coating. [EMIM] [DCN] exhibited a better wear reduction than [BMIM] [TCC] on CrN, and its friction coefficient was higher than that of [BMIM] [TCC]. DLC coatings with [EMIM] [DCN] exhibited better lubricity than with [BMIM] [TCC], and the combination of H-free DLC and [EMIM] [DCN] particularly showed excellent lubricity. XPS analysis showed that two kinds of nitrogen compounds were on the sliding surface of H-free DLC lubricated with [EMIM] [DCN]. [ABSTRACT FROM AUTHOR]

Abstract: We have investigated structural and surface property of transparent conductive Nb-doped titanium oxides (TNO) thin film with high conductivity of 10−4 Ωcm order which were made by RF-magnetron sputtering at high deposition rates followed by an annealing in vacuum. The grain sizes of TNO evaluated by atomic force microscope were found to become larger by annealing at temperature higher than 500°C. The measured work functions of the TNO films using ultra-violet light photoelectron spectroscopy were 5.02–5.47eV, and depended on TNO grain size and on the amount of surface weakly bound oxygen that was estimated from peak area intensities of O(1s) X-ray photoelectron spectra. [ABSTRACT FROM AUTHOR]

Abstract: The formation of self-assembled monolayer and multilayer using redox-active Ru complex molecules with phosphonic acids on SiO2 surface has been examined using X-ray photoelectron spectroscopy (XPS), ellipsometry, and time of flight secondary mass-ion spectroscopy (TOF-SIMS). We found that an introduction of a Zr adlayer leads to higher surface molecular density of Ru complex SAMs on the SiO2 surface, compared to that of obtained from the direct adsorption of Ru complex monolayer on the SiO2 surface. We further tried to fabricate a multilayer film using this molecule with Zr(IV) ion acting as a chemical glue by a successive immersion process. The XPS data revealed that the molecular densities of the multilayers were also higher for the immobilization with Zr adlayer between Ru complex and SiO2 surface than those without the Zr adlayer, suggesting that Zr adlayer is effective in forming highly packed molecular layer of phosphonic acids on SiO2 surface. We found the film growth reached a saturation point after 6 layers on the SiO2 surface. The film growth saturation can be explained by a molecular domain boundary effect encountered due to the large tilt angle of the molecular layer. [Copyright &y& Elsevier]

Abstract: Nano-Si3N4 particles were electrodeposited with nickel on copper substrate from a Ni bath. The friction and wear properties of the Ni/Si3N4 composite coating were evaluated while being lubricated with several various oils using a ball-on-disk sliding tester. The morphologies of the worn surfaces were observed using a scanning electron microscope. The chemical states of several typical elements on the worn surfaces were examined by means of X-ray photoelectron spectroscopy (XPS). Results indicated that the electrodeposited Ni/Si3N4 composition coating had excellent tribological properties while being lubricated with the ionic liquid. This was partly attributed to the high hardness of the electrodeposited nickel composite coating containing nano-sized Si3N4 and the tribochemical reaction between the lubricant and the sliding surface. [Copyright &y& Elsevier]

A correction to the article "Tribological Performance of Halogen-Free Ionic Liquids as Lubricants of Hard Coatings and Ceramics" that was published online in the July 4, 2013 issue is presented.