Pectin Nanoporous Structures Prepared via Salt-Induced Phase Separation and Ambient Azeotropic Evaporation Processes

Polysaccharide nanoporous structures are suitable for various applications, ranging from biomedical scaffolds to adsorption materials, owing to their biocompatibility and large surface areas. Pectin, in particular, can create 3D nanoporous structures in aqueous solutions by binding with calcium cations and creating nanopores by phase separation; this process involves forming hydrogen bonds between alcohols and pectin chains in water and alcohol mixtures and the resulting penetration of alcohols into calcium-bound pectin gels. However, owing to the dehydration and condensation of polysaccharide chains during drying, it has proven to be challenging to maintain the 3D nanoporous structure without using a freeze-drying process or supercritical fluid. Herein, we report a facile method for creating polysaccharide-based xerogels, involving the co-evaporation of water with a nonsolvent (e.g., a low-molecular-weight hydrophobic alcohol such as isopropyl or n-propyl alcohol) at ambient conditions. Experiments and coarse-grained molecular dynamics simulations confirmed that salt-induced phase separation and hydrogen bonding between hydrophobic alcohols and pectin chains were the dominant processes in mixtures of pectin, water, and hydrophobic alcohols. Furthermore, the azeotropic evaporation of water and alcohol mixed in approximately 1:1 molar ratios was maintained during the natural drying process under ambient conditions, preventing the hydration and aggregation of the hydrophilic pectin chains. These results introduce a simple and convenient process to produce 3D polysaccharide xerogels under ambient conditions.

Anillin-related Mid1 as an adaptive and multimodal contractile ring anchoring protein: A simulation study

Cytokinesis of animal and fungi cells depends crucially on the anillin scaffold proteins. Fission yeast anillin-related Mid1 anchors cytokinetic ring precursor nodes to the membrane. However, it is unclear if both of its Pleckstrin Homology (PH) and C2 C-terminal domains bind to the membrane as monomers or dimers, and if one domain plays a dominant role. We studied Mid1 membrane binding with all-atom molecular dynamics near a membrane with yeast-like lipid composition. In simulations with the full C terminal region started away from the membrane, Mid1 binds through the disordered L3 loop of C2 in a vertical orientation, with the PH away from the membrane. However, a configuration with both C2 and PH initially bound to the membrane remains associated with the membrane. Simulations of C2-PH dimers show extensive asymmetric membrane contacts. These multiple modes of binding may reflect Mid1's multiple interactions with membranes, node proteins, and ability to sustain mechanical forces.

Accurate Force Fields for Atomistic Simulations of Oxides, Hydroxides, and Organic Hybrid Materials up to the Micrometer Scale

The simulation of metals, oxides, and hydroxides can accelerate the design of therapeutics, alloys, catalysts, cement-based materials, ceramics, bioinspired composites, and glasses. Here we introduce the INTERFACE force field (IFF) and surface models for α-Al2O3, α-Cr2O3, α-Fe2O3, NiO, CaO, MgO, β-Ca(OH)2, β-Mg(OH)2, and β-Ni(OH)2. The force field parameters are nonbonded, including atomic charges for Coulomb interactions, Lennard-Jones (LJ) potentials for van der Waals interactions with 12-6 and 9-6 options, and harmonic bond stretching for hydroxide ions. The models outperform DFT calculations and earlier atomistic models (Pedone, ReaxFF, UFF, CLAYFF) up to 2 orders of magnitude in reliability, compatibility, and interpretability due to a quantitative representation of chemical bonding consistent with other compounds across the periodic table and curated experimental data for validation. The IFF models exhibit average deviations of 0.2% in lattice parameters, <10% in surface energies (to the extent known), and 6% in bulk moduli relative to experiments. The parameters and models can be used with existing parameters for solvents, inorganic compounds, organic compounds, biomolecules, and polymers in IFF, CHARMM, CVFF, AMBER, OPLS-AA, PCFF, and COMPASS, to simulate bulk oxides, hydroxides, electrolyte interfaces, and multiphase, biological, and organic hybrid materials at length scales from atoms to micrometers. The nonbonded character of the models also enables the analysis of mixed oxides, glasses, and certain chemical reactions, and well-performing nonbonded models for silica phases, SiO2, are introduced. Automated model building is available in the CHARMM-GUI Nanomaterial Modeler. We illustrate applications of the models to predict the structure of mixed oxides, and energy barriers of ion migration, as well as binding energies of water and organic molecules in outstanding agreement with experimental data and calculations at the CCSD(T) level. Examples of model building for hydrated, pH-sensitive oxide surfaces to simulate solid-electrolyte interfaces are discussed.

CHARMM-GUI Multicomponent Assembler for Modeling and Simulation of Complex Multicomponent Systems

Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. We demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to facilitate innovative studies of complex interactions between small (organic and inorganic) molecules, biomacromolecules, polymers, and nanomaterials.

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein-lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.

Anillin Related Mid1 as an Adaptive and Multimodal Contractile Ring Anchoring Protein: A Simulation Study

The organization of the cytokinetic ring at the cell equator of dividing animal and fungi cells depends crucially on the anillin scaffold proteins. In fission yeast, anillin related Mid1 binds to the plasma membrane and helps anchor and organize a medial broad band of cytokinetic nodes, which are the precursors of the contractile ring. Similar to other anillins, Mid1 contains a C terminal globular domain with two potential regions for membrane binding, the Pleckstrin Homology (PH) and C2 domains, and an N terminal intrinsically disordered region that is strongly regulated by phosphorylation. Previous studies have shown that both PH and C2 domains can associate with the membrane, preferring phosphatidylinositol-(4,5)-bisphosphate (PIP 2 ) lipids. However, it is unclear if they can simultaneously bind to the membrane in a way that allows dimerization or oligomerization of Mid1, and if one domain plays a dominant role. To elucidate Mid1's membrane binding mechanism, we used the available structural information of the C terminal region of Mid1 in all-atom molecular dynamics (MD) near a membrane with a lipid composition based on experimental measurements (including PIP 2 lipids). The disordered L3 loop of C2, as well as the PH domain, separately bind the membrane through charged lipid contacts. In simulations with the full C terminal region started away from the membrane, Mid1 binds through the L3 loop and is stabilized in a vertical orientation with the PH domain away from the membrane. However, a configuration with both C2 and PH initially bound to the membrane remains associated with the membrane. These multiple modes of binding may reflect Mid1's multiple interactions with membranes and other node proteins, and ability to sustain mechanical forces.

Suppression of Lung Cancer Malignancy by Micellized siRNA through Cell Cycle Arrest

UBA6-specific E2 conjugation enzyme 1 (USE1) is frequently overexpressed in lung cancer patients. Moreover, the critical role of USE1 in the progression of human lung cancer is also indicated. As the next step, the authors aim to develop USE1-targeted therapeutic agents based on RNA interference (RNAi). In this study, a lipid-modified DNA carrier, namely U4T, which consists of four consecutive dodec-1-ynyluracil (U) nucleobases to increase the cell permeability of siRNA targeting of USE1 is introduced. The U4Ts aggregate to form micelles, and the USE1-silencing siRNA-incorporated soft spherical nucleic acid aggregate (siSNA) can be created simply through base-pairing with siRNA. Treatment with siSNA is effective in suppressing tumor growth in vivo as well as cell proliferation, migration, and invasion of lung cancer cells. Furthermore, siSNA inhibited tumor cell growth by inducing cell cycle arrest in the G1 phase and apoptosis. Thus, the anti-tumor efficacy of siSNA in lung cancer cell lines and that siSNA possesses effective cell-penetrating ability without using cationic transfection moieties are confirmed. Collectively, these results suggest that siSNA can be applied to the clinical application of RNAi-based therapeutics for lung cancer treatment.

Structural basis for Y2 receptor-mediated neuropeptide Y and peptide YY signaling

Neuropeptide Y (NPY) and its receptors are expressed in various human tissues including the brain where they regulate appetite and emotion. Upon NPY stimulation, the neuropeptide Y1 and Y2 receptors (Y₁R and Y₂R, respectively) activate G_I signaling, but their physiological responses to food intake are different. In addition, deletion of the two N-terminal amino acids of peptide YY (PYY(3-36)), the endogenous form found in circulation, can stimulate Y₂R but not Y₁R, suggesting that Y₁R and Y₂R may have distinct ligand-binding modes. Here, we report the cryo-electron microscopy structures of the PYY(3-36)‒Y₂R‒G_i and NPY‒Y₂R‒G_i complexes. Using cell-based assays, molecular dynamics simulations, and structural analysis, we revealed the molecular basis of the exclusive binding of PYY(3-36) to Y₂R. Furthermore, we demonstrated that Y₂R favors G protein signaling over β-arrestin signaling upon activation, whereas Y₁R does not show a preference between these two pathways.

CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems

Molecular modeling and simulation are invaluable tools for nanoscience that predict mechanical, physicochemical, and thermodynamic properties of nanomaterials and provide molecular-level insight into underlying mechanisms. However, building nanomaterial-containing systems remains challenging due to the lack of reliable and integrated cyberinfrastructures. Here we present Nanomaterial Modeler in CHARMM-GUI, a web-based cyberinfrastructure that provides an automated process to generate various nanomaterial models, associated topologies, and configuration files to perform state-of-the-art molecular dynamics simulations using most simulation packages. The nanomaterial models are based on the interface force field, one of the most reliable force fields (FFs). The transferability of nanomaterial models among the simulation programs was assessed by single-point energy calculations, which yielded 0.01% relative absolute energy differences for various surface models and equilibrium nanoparticle shapes. Three widely used Lennard-Jones (LJ) cutoff methods are employed to evaluate the compatibility of nanomaterial models with respect to conventional biomolecular FFs: simple truncation at r = 12 Å (12 cutoff), force-based switching over 10 to 12 Å (10-12 fsw), and LJ particle mesh Ewald with no cutoff (LJPME). The FF parameters with these LJ cutoff methods are extensively validated by reproducing structural, interfacial, and mechanical properties. We find that the computed density and surface energies are in good agreement with reported experimental results, although the simulation results increase in the following order: 10-12 fsw <12 cutoff < LJPME. Nanomaterials in which LJ interactions are a major component show relatively higher deviations (up to 4% in density and 8% in surface energy differences) compared with the experiment. Nanomaterial Modeler's capability is also demonstrated by generating complex systems of nanomaterial-biomolecule and nanomaterial-polymer interfaces with a combination of existing CHARMM-GUI modules. We hope that Nanomaterial Modeler can be used to carry out innovative nanomaterial modeling and simulations to acquire insight into the structure, dynamics, and underlying mechanisms of complex nanomaterial-containing systems.

CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids

A lipid nanoparticle (LNP) formulation is a state-of-the-art delivery system for genetic drugs such as DNA, messenger RNA, and small interfering RNA, which is successfully applied to COVID-19 vaccines and gains tremendous interest in therapeutic applications. Despite its importance, a molecular-level understanding of the LNP structures and dynamics is still lacking, which makes rational LNP design almost impossible. In this work, we present an extension of CHARMM-GUI Membrane Builder to model and simulate all-atom LNPs with various (ionizable) cationic lipids and PEGylated lipids (PEG-lipids). These new lipid types can be mixed with any existing lipid types with or without a biomolecule of interest, and the generated systems can be simulated using various molecular dynamics engines. As a first illustration, we considered model LNP membranes with DLin-KC2-DMA (KC2) or DLin-MC3-DMA (MC3) without PEG-lipids. The results from these model membranes are consistent with those from the two previous studies, albeit with mild accumulation of neutral MC3 in the bilayer center. To demonstrate Membrane Builder's capability of building a realistic LNP patch, we generated KC2- or MC3-containing LNP membranes with high concentrations of cholesterol and ionizable cationic lipids together with 2 mol % PEG-lipids. We observe that PEG-chains are flexible, which can be more preferentially extended laterally in the presence of cationic lipids due to the attractive interactions between their head groups and PEG oxygen. The presence of PEG-lipids also relaxes the lateral packing in LNP membranes, and the area compressibility modulus (KA) of LNP membranes with cationic lipids fit into typical KA of fluid-phase membranes. Interestingly, the interactions between PEG oxygen and the head group of ionizable cationic lipids induce a negative curvature. We hope that this LNP capability in Membrane Builder can be useful to better characterize various LNPs with or without genetic drugs for rational LNP design.

Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a public health crisis, and the vaccines that can induce highly potent neutralizing antibodies are essential for ending the pandemic. The spike (S) protein on the viral envelope mediates human angiotensin-converting enzyme 2 binding and thus is the target of a variety of neutralizing antibodies. In this work, we built various S trimer-antibody complex structures on the basis of the fully glycosylated S protein models described in our previous work and performed all-atom molecular dynamics simulations to gain insight into the structural dynamics and interactions between S protein and antibodies. Investigation of the residues critical for S-antibody binding allows us to predict the potential influence of mutations in SARS-CoV-2 variants. Comparison of the glycan conformations between S-only and S-antibody systems reveals the roles of glycans in S-antibody binding. In addition, we explored the antibody binding modes and the influences of antibody on the motion of S protein receptor binding domains. Overall, our analyses provide a better understanding of S-antibody interactions, and the simulation-based S-antibody interaction maps could be used to predict the influences of S mutation on S-antibody interactions, which will be useful for the development of vaccine and antibody-based therapy.

Carrier-free micellar CpG interacting with cell membrane for enhanced immunological treatment of HIV-1

Unmethylated CpG motifs activate toll-like receptor 9 (TLR9), leading to sequence- and species-specific immune stimulation. Here, we engineered a CpG oligodeoxyribonucleotide (ODN) with multiple hydrophobic moieties, so-called lipid-modified uracil, which resulted in a facile micelle formation of the stimulant. The self-assembled CpG nanostructure (U4CpG) containing the ODN 2216 sequence was characterized by various spectroscopic and microscopic methods together with molecular dynamics simulations. Next, we evaluated the nano-immunostimulant for enhancement of anti-HIV immunity. U4CpG treatment induced activation of plasmacytoid dendritic cells (pDCs) and natural killer (NK) cells in healthy human peripheral blood, which produced type I interferons (IFNs) and IFN-γ in human peripheral blood mononuclear cells (PBMCs). Moreover, we validated the activation and promotion efficacy of U4CpG in patient-derived blood cells, and HIV-1 spread was significantly suppressed by a low dosage of the immunostimulant. Furthermore, U4CpG-treated PBMC cultured medium elicited transcription of latent HIV-1 in U1 cells indicating that U4CpG reversed HIV-1 latency. Thus, the functions of U4CpG in eradicating HIV-1 by enhancing immunity and reversing latency make the material a potential candidate for clinical studies dealing with viral infection.

CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids

A lipid nanoparticle (LNP) formulation is a state-of-the-art delivery system for genetic drugs such as DNA, mRNA, and siRNA, which is successfully applied to COVID-19 vaccines and gains tremendous interest in therapeutic applications. Despite its importance, a molecular-level understanding of the LNP structures and dynamics is still lacking, which makes a rational LNP design almost impossible. In this work, we present an extension of CHARMM-GUI Membrane Builder to model and simulate all-atom LNPs with various (ionizable) cationic lipids and PEGylated lipids (PEG-lipids). These new lipid types can be mixed with any existing lipid types with or without a biomolecule of interest, and the generated systems can be simulated using various molecular dynamics engines. As a first illustration, we considered model LNP membranes with DLin-KC2-DMA (KC2) or DLin-MC3-DMA (MC3) without PEG-lipids. The results from these model membranes are consistent with those from the two previous studies albeit with mild accumulation of neutral MC3 in the bilayer center. To demonstrate Membrane Builder's capability of building a realistic LNP patch, we generated KC2- or MC3-containing LNP membranes with high concentrations of cholesterol and ionizable cationic lipids together with 2 mol% PEG-lipids. We observe that PEG-chains are flexible, which can be more preferentially extended laterally in the presence of cationic lipids due to the attractive interactions between their head groups and PEG oxygen. The presence of PEG-lipids also relaxes the lateral packing in LNP membranes, and the area compressibility modulus (KA) of LNP membranes with cationic lipids fit into typical KA of fluid-phase membranes. Interestingly, the interactions between PEG oxygen and head group of ionizable cationic lipids induce a negative curvature. We hope that this LNP capability in Membrane Builder can be useful to better characterize various LNPs with or without genetic drugs for a rational LNP design.

Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a public health crisis, and the vaccines that can induce highly potent neutralizing antibodies are essential for ending the pandemic. The spike (S) protein on the viral envelope mediates human angiotensin-converting enzyme 2 (ACE2) binding and thus is the target of a variety of neutralizing antibodies. In this work, we built various S trimer-antibody complex structures on the basis of the fully glycosylated S protein models described in our previous work, and performed all-atom molecular dynamics simulations to get insight into the structural dynamics and interactions between S protein and antibodies. Investigation of the residues critical for S-antibody binding allows us to predict the potential influence of mutations in SARS-CoV-2 variants. Comparison of the glycan conformations between S-only and S-antibody systems reveals the roles of glycans in S-antibody binding. In addition, we explored the antibody binding modes, and the influences of antibody on the motion of S protein receptor binding domains. Overall, our analyses provide a better understanding of S-antibody interactions, and the simulation-based S-antibody interaction maps could be used to predict the influences of S mutation on S-antibody interactions, which will be useful for the development of vaccine and antibody-based therapy.

CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers

Molecular modeling and simulations are invaluable tools for polymer science and engineering, which predict physicochemical properties of polymers and provide molecular-level insight into the underlying mechanisms. However, building realistic polymer systems is challenging and requires considerable experience because of great variations in structures as well as length and time scales. This work describes Polymer Builder in CHARMM-GUI (http://www.charmm-gui.org/input/polymer), a web-based infrastructure that provides a generalized and automated process to build a relaxed polymer system. Polymer Builder not only provides versatile modeling methods to build complex polymer structures, but also generates realistic polymer melt and solution systems through the built-in coarse-grained model and all-atom replacement. The coarse-grained model parametrization is generalized and extensively validated with various experimental data and all-atom simulations. In addition, the capability of Polymer Builder for generating relaxed polymer systems is demonstrated by density calculations of 34 homopolymer melt systems, characteristic ratio calculations of 170 homopolymer melt systems, a morphology diagram of poly(styrene-b-methyl methacrylate) block copolymers, and self-assembly behavior of amphiphilic poly(ethylene oxide-b-ethylethane) block copolymers in water. We hope that Polymer Builder is useful to carry out innovative and novel polymer modeling and simulation research to acquire insight into structures, dynamics, and underlying mechanisms of complex polymer-containing systems.

Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane

The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates host cell entry by binding to angiotensin-converting enzyme 2 (ACE2) and is considered the major target for drug and vaccine development. We previously built fully glycosylated full-length SARS-CoV-2 S protein models in a viral membrane including both open and closed conformations of the receptor-binding domain (RBD) and different templates for the stalk region. In this work, multiple μs-long all-atom molecular dynamics simulations were performed to provide deeper insights into the structure and dynamics of S protein and glycan functions. Our simulations reveal that the highly flexible stalk is composed of two independent joints and most probable S protein orientations are competent for ACE2 binding. We identify multiple glycans stabilizing the open and/or closed states of the RBD and demonstrate that the exposure of antibody epitopes can be captured by detailed antibody–glycan clash analysis instead of commonly used accessible surface area analysis that tends to overestimate the impact of glycan shielding and neglect possible detailed interactions between glycan and antibodies. Overall, our observations offer structural and dynamic insights into the SARS-CoV-2 S protein and potentialize for guiding the design of effective antiviral therapeutics.

Structure, Dynamics, and Interactions of GPI-Anchored Human Glypican-1 with Heparan Sulfates in a Membrane

Glypican-1 and its heparan sulfate (HS) chains play important roles in modulating many biological processes including growth factor signaling. Glypican-1 is bound to a membrane surface via a glycosylphosphatidylinositol (GPI)-anchor. In this study, we used all-atom molecular modeling and simulation to explore the structure, dynamics, and interactions of GPI-anchored glypican-1, three HS chains, membranes, and ions. The folded glypican-1 core structure is stable, but has substantial degrees of freedom in terms of movement and orientation with respect to the membrane due to the long unstructured C-terminal region linking the core to the GPI-anchor. With unique structural features depending on the extent of sulfation, high flexibility of HS chains can promote multi-site interactions with surrounding molecules near and above the membrane. This study is a first step toward all-atom molecular modeling and simulation of the glycocalyx, as well as its modulation of interactions between growth factors and their receptors.

Demetylation of the sex-determining region Y gene promoter and incidence of disorder of sex development in cloned dog males

Canine cloning is occasionally accompanied by abnormal sexual development. Some male donor cells produce cloned pups with female external genitalia and complete male gonadal dysgenesis, which is classified as an XY disorder of sex development (XY DSD). In this study, we examine the potential of 5-aza-2'-deoxycytidine (5-aza-dC), a DNA methyltransferase inhibitor, to reduce the phenotypic abnormality XY DSD in somatic cell nuclear transfer (SCNT)- derived pups. We used a 9-year-old normal male German Shepherd dog as a cell donor. Donor cells were treated with 10 nM 5-aza-dC for 4 days before being used for SCNT. At the same stage of cell development, significantly lower levels of DNA methylation of the sex-determining region Y (SRY) promoter was observed in the treated donor cells compared to that in the untreated cells (95.2% versus 53.3% on day 4 for the control and treated groups, respectively). No significant differences were observed in the control or treatment groups concerning fusion rate, pregnancy rate (30 days or entire period), the number of pups, or the incidence of XY DSD. However, more XY DSD dogs were observed in the control group (31.25%) than in the treatment group (14.29%). Hypermethylation of the SRY promoter was observed in the XY DSD cloned pups in both the treatment (84.8%) and control groups (91.1 ± 1.4%) compared to the methylation level in the phenotypically normal male pups of the treatment (23.2 ± 20.9%) and control groups (39.1 ± 20.1%). These results suggest that 5-aza-dC treatment of donor cells can reduce the methylation level of the SRY promoter in donor cells, and thus, 5-aza-dC is advantageous for reducing the incidence of XY DSD in canine cloning.

Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane

This technical study describes all-atom modeling and simulation of a fully glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB: 6VSB and 6VXX, full-length S protein structures were modeled using template-based modeling, de-novo protein structure prediction, and loop modeling techniques in GALAXY modeling suite. Then, using the recently determined most occupied glycoforms, 22 N-glycans and 1 O-glycan of each monomer were modeled using Glycan Reader & Modeler in CHARMM-GUI. These fully glycosylated full-length S protein model structures were assessed and further refined against the low-resolution data in their respective experimental maps using ISOLDE. We then used CHARMM-GUI Membrane Builder to place the S proteins in a viral membrane and performed all-atom molecular dynamics simulations. All structures are available in CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19) so that researchers can use these models to carry out innovative and novel modeling and simulation research for the prevention and treatment of COVID-19.

Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane

This technical study describes all-atom modeling and simulation of a fully-glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB:6VSB and 6VXX, full-length S protein structures were modeled using template-based modeling, de-novo protein structure prediction, and loop modeling techniques in GALAXY modeling suite. Then, using the recently-determined most occupied glycoforms, 22 N-glycans and 1 O-glycan of each monomer were modeled using Glycan Reader & Modeler in CHARMM-GUI. These fully-glycosylated full-length S protein model structures were assessed and further refined against the low-resolution data in their respective experimental maps using ISOLDE. We then used CHARMM-GUI Membrane Builder to place the S proteins in a viral membrane and performed all-atom molecular dynamics simulations. All structures are available in CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19), so researchers can use these models to carry out innovative and novel modeling and simulation research for the prevention and treatment of COVID-19.

Formation of nanopores in DiynePC-DPPC complex lipid bilayers triggered by on-demand photo-polymerization

Vesicles have unique characteristics that enable the release of drugs as well as encapsulation while maintaining biocompatibility. A photo-polymerizable liposome composed of 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine (23:2 DiynePC) has been investigated as vehicles for triggered delivery of drugs to cells. In this study, we confirmed for the first time that supported lipid bilayers (SLBs) prepared with a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC)/DiynePC mixture generated pores ca. 100-300 nm in size on the membrane after UV polymerization. This direct observation was done by analyzing the SLBs formed with the DPPC/DiynePC mixture by employing atomic force microscopy (AFM) in a liquid environment. However, photo-polymerization did not occur in the 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)/DiynePC mixed bilayer and pores were not formed. A theoretical study was performed to explore the phase behavior of the lipid mixtures. A coarse-grained model of DiynePC was developed that is comparable with the Martini force field; the parameters were validated against atomistic simulations. Transition from fluidic to gel phase was observed only when DiynePC was mixed with DPPC, whereas the DOPC mixture remained fluidic over the entire domain. This implies a correlation between the formation of DiynePC-rich gel phase domains and the generation of pores after polymerization. The size of the pores were found to be controlled by the amount of polymerizable lipid which results in higher release rate of encapsulated calcein from the vesicles with larger pores.

Properties of Dye-Sensitized Solar Cells Using Carbon Nanowall Counter Electrodes

This research investigates plasma-treated and metal-coated carbon nanowalls (CNWs) for use as counter electrodes of dye-sensitized solar cells (DSSCs). The CNWs were synthesized on a fluorine-tin-oxide (FTO) glass substrate using the microwave plasma-enhanced chemical vapor deposition (PECVD) system with methane (CH4) gas. The post-plasma treatment was performed on the CNWs with hydrogen (H2) plasma using PECVD, and the CNWs were sputter-coated with metal films using the RF magnetron sputtering system with a four-inch tungsten (W) target. Then the post-plasma-treated and metal-coated CNWs were used as counter electrodes for the fabrication of the DSSCs. Field-emission scanning electron microscopy (FE-SEM) was performed to obtain cross-sectional and planar images of the grown CNWs. The energy conversion efficiencies of the DSSCs manufactured using the post-plasma-treated and metal-layer-coated CNWs as the counter electrodes were measured.

Reaction Gas Ratio Effect on the Growth of a Diamond Film Using Microwave Plasma-Enhanced Chemical Vapor Deposition

In this study, diamond films were prepared using the microwave plasma-enhanced chemical vapor deposition (PECVD) system, which included a DC bias system to enhance the nucleation of the films. The films were synthesized on Si wafers with different ratios of methane (CH4) and hydrogen (H2) gases. We have studied the effects of the CH4-to-H2 ratio on the structural and optical properties of diamond films. The thickness and surface profile of the films were characterized via field emission scanning electron microscopy (FE-SEM). Raman was used to investigate the structural properties of the diamond films. The refractive indexes as functions of the CH4-to-H2 ratio were measured using an ellipsometer. The FE-SEM analysis showed that the 3 and 5 sccm CH4 created diamond films. The Raman analysis indicated that a nanocrystalline diamond film was formed at 3 sccm; a general diamond film, at 5 sccm; and films similar to the a-C:H film, at 7 sccm. The ellipsometer measurement showed that the refractive index of the synthesized diamond film was around 2.42 at 3 sccm. This value decreased as the CH4 volume increased.

Study of B Meson Production in p+Pb Collisions at √[S(NN)]=5.02 TeV Using Exclusive Hadronic Decays

The production cross sections of the B^{+}, B^{0}, and B_{s}^{0} mesons, and of their charge conjugates, are measured via exclusive hadronic decays in p+Pb collisions at the center-of-mass energy sqrt[s_{NN}]=5.02  TeV with the CMS detector at the CERN LHC. The data set used for this analysis corresponds to an integrated luminosity of 34.6  nb^{-1}. The production cross sections are measured in the transverse momentum range between 10 and 60  GeV/c. No significant modification is observed compared to proton-proton perturbative QCD calculations scaled by the number of incoherent nucleon-nucleon collisions. These results provide a baseline for the study of in-medium b quark energy loss in Pb+Pb collisions.

Association between prolonged breastfeeding and bone mineral density and osteoporosis in postmenopausal women: KNHANES 2010-2011

This study showed that a negative correlation between duration of breastfeeding and bone mineral density (BMD) in the lumbar spine and prolonged breastfeeding is an independent risk for osteoporosis in postmenopausal women. The present study suggests that postmenopausal women with a history of prolonged breastfeeding require more careful screening for osteoporosis.

INTRODUCTION

Several studies suggest that breastfeeding and childbirth lead to maternal calcium loss and a decline in BMD. While the association between breastfeeding and BMD immediately after weaning is well-established, the effects of breastfeeding on postmenopausal women have been controversial. The aim of this study was to examine the effects of breastfeeding on bone mineral density (BMD) and the prevalence of osteoporosis in postmenopausal women.

METHODS

The present study was a cross-sectional survey based on the Korea National Health and Nutrition Examination Survey (KNHANES) 2010 and 2011 data. The association between breastfeeding and BMD and osteoporosis was examined in 1222 postmenopausal women.

RESULTS

The duration of breastfeeding and BMD in the lumbar spine showed a negative correlation. The association between duration of breastfeeding and BMD remained significant after adjustment for reproductive factors and other confounding factors (P = 0.008). However, the number of deliveries and age at the time of delivery did not correlate with BMD at any site after adjustment. Moreover, the prevalence of osteoporosis in postmenopausal women with a history of prolonged breastfeeding was significantly higher than that in women with a short history of breastfeeding (≥37 months, OR = 3.292; 95 % CI 1.485-7.299). The prevalence of lumbar spine fracture showed a significant increasing trend with the increase in the duration of breastfeeding.

CONCLUSION

Prolonged breastfeeding was significantly associated with low BMD in the lumbar spine and higher prevalence of osteoporosis. However, the number of deliveries or age at the time of childbirth did not influence BMD.

Evidence for Collective Multiparticle Correlations in p-Pb Collisions

The second-order azimuthal anisotropy Fourier harmonics, v2, are obtained in p-Pb and PbPb collisions over a wide pseudorapidity (η) range based on correlations among six or more charged particles. The p-Pb data, corresponding to an integrated luminosity of 35  nb-1, were collected during the 2013 LHC p-Pb run at a nucleon-nucleon center-of-mass energy of 5.02  TeV by the CMS experiment. A sample of semiperipheral PbPb collision data at √sNN=2.76  TeV, corresponding to an integrated luminosity of 2.5  μb-1 and covering a similar range of particle multiplicities as the p-Pb data, is also analyzed for comparison. The six- and eight-particle cumulant and the Lee-Yang zeros methods are used to extract the v2 coefficients, extending previous studies of two- and four-particle correlations. For both the p-Pb and PbPb systems, the v2 values obtained with correlations among more than four particles are consistent with previously published four-particle results. These data support the interpretation of a collective origin for the previously observed long-range (large Δη) correlations in both systems. The ratios of v2 values corresponding to correlations including different numbers of particles are compared to theoretical predictions that assume a hydrodynamic behavior of a p-Pb system dominated by fluctuations in the positions of participant nucleons. These results provide new insights into the multiparticle dynamics of collision systems with a very small overlapping region.

Measurement of J/ψ and ψ(2S) Prompt Double-Differential Cross Sections in pp Collisions at sqrt[s]=7 TeV

The double-differential cross sections of promptly produced J/ψ and ψ(2S) mesons are measured in pp collisions at sqrt[s]=7 TeV, as a function of transverse momentum p_{T} and absolute rapidity |y|. The analysis uses J/ψ and ψ(2S) dimuon samples collected by the CMS experiment, corresponding to integrated luminosities of 4.55 and 4.90 fb^{-1}, respectively. The results are based on a two-dimensional analysis of the dimuon invariant mass and decay length, and extend to p_{T}=120 and 100 GeV for the J/ψ and ψ(2S), respectively, when integrated over the interval |y|<1.2. The ratio of the ψ(2S) to J/ψ cross sections is also reported for |y|<1.2, over the range 10<p_{T}<100 GeV. These are the highest p_{T} values for which the cross sections and ratio have been measured.

Responses of osteoblastic cell line MC3T3-E1 cell to the calcium channel blocker diltiazem and verapamil

The effects of the calcium channel blockers, diltiazem and verapamil, on osteoblastic functions were investigated in cultured osteoblastic cells MC3T3-E1. DNA synthesis was evaluated by the incorporation of [3H]thymidine, and collagen synthesis by measuring the incorporation of [3H]proline into collagenase-digestible protein (CDP) and noncollagen protein (NCP). Diltiazem inhibited the DNA synthesis of osteoblastic cells by up to 57.6 and 54.6% at concentrations of 25 and 50 microM. Verapamil also significantly inhibited DNA synthesis by up to 61.6 and 40.9% at concentrations of 25 and 50 microM. The percent control of CDP formation were decreased by up to 76.7% in 5 microM and 44.3% in 50 microM of diltiazem. Verapamil also decreased CDP synthesis to 49.7% at 10 microM and 32.6% at 50 microM. NCP synthesis was decreased by the calcium channel blocker but inhibition of the CDP formation was greater than that of NCP. The calculated percent collagen synthesis was decreased at a calcium channel blocker concentration of 10 microM. The inhibitory effects of diltiazem and verapamil on percent collagen synthesis were not reversed by increasing the calcium concentration of culture media by either 1 or 5 mM. From this study, we conclude that calcium channel blockers have a direct inhibitory effect on osteoblastic function. Long-term administration of diltiazem or verapamil produces adverse effects on normal bone metabolism.

Search for monotop signatures in proton-proton collisions at √s=8 TeV

Results are presented from a search for new decaying massive particles whose presence is inferred from an imbalance in transverse momentum and which are produced in association with a single top quark that decays into a bottom quark and two light quarks. The measurement is performed using 19.7  fb^{-1} of data from proton-proton collisions at a center-of-mass energy of 8 TeV, collected with the CMS detector at the CERN LHC. No deviations from the standard model predictions are observed and lower limits are set on the masses of new invisible bosons. In particular, scalar and vector particles, with masses below 330 and 650 GeV, respectively, are excluded at 95% confidence level, thereby substantially extending a previous limit published by the CDF Collaboration.

Search for displaced supersymmetry in events with an electron and a muon with large impact parameters

A search for new long-lived particles decaying to leptons is presented using proton-proton collisions produced by the LHC at √[s]=8  TeV. Data used for the analysis were collected by the CMS detector and correspond to an integrated luminosity of 19.7  fb(-1). Events are selected with an electron and muon with opposite charges that both have transverse impact parameter values between 0.02 and 2 cm. The search has been designed to be sensitive to a wide range of models with nonprompt e-μ final states. Limits are set on the "displaced supersymmetry" model, with pair production of top squarks decaying into an e-μ final state via R-parity-violating interactions. The results are the most restrictive to date on this model, with the most stringent limit being obtained for a top squark lifetime corresponding to cτ=2  cm, excluding masses below 790 GeV at 95% confidence level.

Study of vector boson scattering and search for new physics in events with two same-sign leptons and two jets

A study of vector boson scattering in pp collisions at a center-of-mass energy of 8 TeV is presented. The data sample corresponds to an integrated luminosity of 19.4  fb(-1) collected with the CMS detector. Candidate events are selected with exactly two leptons of the same charge, two jets with large rapidity separation and high dijet mass, and moderate missing transverse energy. The signal region is expected to be dominated by electroweak same-sign W-boson pair production. The observation agrees with the standard model prediction. The observed significance is 2.0 standard deviations, where a significance of 3.1 standard deviations is expected based on the standard model. Cross section measurements for W(±)W(±) and WZ processes in the fiducial region are reported. Bounds on the structure of quartic vector-boson interactions are given in the framework of dimension-eight effective field theory operators, as well as limits on the production of doubly charged Higgs bosons.

Implementation of secondary stroke prevention protocol for ischaemic stroke patients in primary care

OBJECTIVE

To investigate the effectiveness of a secondary stroke prevention protocol in the general out-patient clinic.

DESIGN

Cohort study with pre- and post-intervention comparisons.

SETTING

Two general out-patient clinics in Hong Kong.

PATIENTS

Ischaemic stroke patients who had long-term follow-up in two clinics were recruited. The patients of one clinic received the intervention (intervention group) and the patients of the second clinic did not receive the intervention (control group). The recruitment period lasted for 6 months from 1 September 2008 to 28 February 2009. The pre-intervention phase data collection started within this 6-month period. The protocol implementation started at the intervention clinic on 1 April 2009. The post-intervention phase data collection started 9 months after the protocol implementation, and ran for 6 months from 1 January 2010 to 30 June 2010.

MAIN OUTCOME MEASURES

Clinical data before and after the intervention, including blood pressure, glycated haemoglobin level, low-density lipoprotein level and prescription pattern, were compared between the two groups to see whether there was enhancement of secondary stroke management.

RESULTS

A total of 328 patients were recruited into the intervention group and 249 into the control group; data of 256 and 210 patients from these groups were analysed, respectively. After intervention, there were significant reductions in mean (± standard deviation) systolic blood pressure (135.2 ± 17.5 mm Hg to 127.7 ± 12.2 mm Hg), glycated haemoglobin level (7.2 ± 1.0% to 6.5 ± 0.8%), and low-density lipoprotein level (3.4 ± 0.8 mmol/L to 2.8 ± 1.3 mmol/L) in the intervention group (all P<0.01). There were no significant reductions in mean systolic blood pressure, glycated haemoglobin level, or low-density lipoprotein level in the control group. There was a significant increase in statin use (P<0.01) in both clinics.

CONCLUSION

Through implementation of a clinic protocol, the standard of care of secondary stroke prevention for ischaemic stroke patients could be improved in a general out-patient clinic.

Measurement of prompt ψ(2S) to J/ψ yield ratios in Pb-Pb and p-p collisions at sqrt[sNN]=2.76 TeV

The ratio between the prompt ψ(2S) and J/ψ yields, reconstructed via their decays into μ+ μ-, is measured in Pb-Pb and p-p collisions at sqrt[sNN]=2.76  TeV. The analysis is based on Pb-Pb and p-p data samples collected by CMS at the Large Hadron Collider, corresponding to integrated luminosities of 150  μb(-1) and 5.4  pb(-1), respectively. The double ratio of measured yields (Nψ(2S)/N(J/ψ))(Pb-Pb)/(Nψ(2S)/N(J/ψ))(p-p) is computed in three Pb-Pb collision centrality bins and two kinematic ranges: one at midrapidity, |y|<1.6, covering the transverse momentum range 6.5<pT<30  GeV/c, and the other at forward rapidity, 1.6<|y|<2.4, extending to lower pT values, 3<pT<30  GeV/c. The centrality-integrated double ratio changes from 0.45±0.13(stat)±0.07(syst) in the first range to 1.67±0.34(stat)±0.27(syst) in the second. This difference is most pronounced in the most central collisions.

Evidence of b-jet quenching in PbPb collisions at √(s(NN))=2.76 TeV

The production of jets associated to bottom quarks is measured for the first time in PbPb collisions at a center-of-mass energy of 2.76 TeV per nucleon pair. Jet spectra are reported in the transverse momentum (p(T)) range of 80-250  GeV/c, and within pseudorapidity |η|<2. The nuclear modification factor (R(AA)) calculated from these spectra shows a strong suppression in the b-jet yield in PbPb collisions relative to the yield observed in pp collisions at the same energy. The suppression persists to the largest values of p(T) studied, and is centrality dependent. The R(AA) is about 0.4 in the most central events, similar to previous observations for inclusive jets. This implies that jet quenching does not have a strong dependence on parton mass and flavor in the jet p(T) range studied.

Observation of the associated production of a single top quark and a W boson in pp collisions at sqrt[s] = 8 TeV

The first observation of the associated production of a single top quark and a W boson is presented. The analysis is based on a data set corresponding to an integrated luminosity of 12.2 fb(-1) of proton-proton collisions at sqrt[s] = 8 TeV recorded by the CMS experiment at the LHC. Events with two leptons and a jet originating from a b quark are selected. A multivariate analysis based on kinematic and topological properties is used to separate the signal from the dominant tt background. An excess consistent with the signal hypothesis is observed, with a significance which corresponds to 6.1 standard deviations above a background-only hypothesis. The measured production cross section is 23.4 ± 5.4 pb, in agreement with the standard model prediction.

Measurement of inclusive W and Z boson production cross sections in pp collisions at sqrt[s] = 8 TeV

A measurement of total and fiducial inclusive W and Z boson production cross sections in pp collisions at sqrt[s] = 8 TeV is presented. Electron and muon final states are analyzed in a data sample collected with the CMS detector corresponding to an integrated luminosity of 18.2 ± 0.5 pb(-1). The measured total inclusive cross sections times branching fractions are σ(pp → WX)×B(W → ℓν) = 12.21 ± 0.03(stat) ± 0.24(syst) ± 0.32(lum) nb and σ(pp → ZX) × B(Z → ℓ+ℓ-) = 1.15 ± 0.01(stat) ± 0.02(syst) ± 0.03(lum) nb for the dilepton mass in the range of 60-120 GeV. The measured values agree with next-to-next-to-leading-order QCD cross section calculations. Ratios of cross sections are reported with a precision of 2%. This is the first measurement of inclusive W and Z boson production in proton-proton collisions at sqrt[s] = 8 TeV.

Measurements of tt spin correlations and top-quark polarization using dilepton final states in pp collisions at sqrt[s]=7 TeV

Spin correlations and polarization in the top quark-antiquark system are measured using dilepton final states produced in pp collisions at the LHC at sqrt[s]=7  TeV. The data correspond to an integrated luminosity of 5.0  fb(-1) collected with the CMS detector. The measurements are performed using events with two oppositely charged leptons (electrons or muons), a significant imbalance in transverse momentum, and two or more jets, where at least one of the jets is identified as originating from a b quark. The spin correlations and polarization are measured through asymmetries in angular distributions of the two selected leptons, unfolded to the parton level. All measurements are found to be in agreement with predictions of the standard model.

Search for top-quark partners with charge 5/3 in the same-sign dilepton final state

A search for the production of heavy partners of the top quark with charge 5/3 is performed in events with a pair of same-sign leptons. The data sample corresponds to an integrated luminosity of 19.5 fb(-1) and was collected at sqrt[s] = 8 TeV by the CMS experiment. No significant excess is observed in the data above the expected background, and the existence of top-quark partners with masses below 800 GeV is excluded at a 95% confidence level, assuming they decay exclusively to tW. This is the first limit on these particles from the LHC, and it is significantly more restrictive than previous limits.

Search for flavor-changing neutral currents in top-quark decays t → Zq in pp collisions at sqrt[s] = 8 TeV

A search for flavor-changing neutral currents in top-quark decays t → Zq is performed in events produced from the decay chain tt → Zq+Wb, where both vector bosons decay leptonically, producing a final state with three leptons (electrons or muons). A data set collected with the CMS detector at the LHC is used, corresponding to an integrated luminosity of 19.7 fb(-1) of proton-proton collisions at a center-of-mass energy of 8 TeV. No excess is seen in the observed number of events relative to the standard model prediction; thus, no evidence for flavor-changing neutral currents in top-quark decays is found. A combination with a previous search at 7 TeV excludes a t → Zq branching fraction greater than 0.05% at the 95% confidence level.

Search for top squark and Higgsino production using diphoton Higgs boson decays

Results are presented of a search for a "natural" supersymmetry scenario with gauge mediated symmetry breaking. It is assumed that only the supersymmetric partners of the top quark (the top squark) and the Higgs boson (Higgsino) are accessible. Events are examined in which there are two photons forming a Higgs boson candidate, and at least two b-quark jets. In 19.7  fb-1 of proton-proton collision data at s=8  TeV, recorded in the CMS experiment, no evidence of a signal is found and lower limits at the 95% confidence level are set, excluding the top squark mass below 360 to 410 GeV, depending on the Higgsino mass.

Relationship between prosthodontic status and nutritional intake in the elderly in Korea: National Health and Nutrition Examination Survey (NHANES IV)

OBJECTIVES

Many health issues have been reported to be associated with poor nutritional status. We sought to examine the association between nutritional intake and oral health status in elderly people.

METHODS

The association between perceived disability in mastication and prosthodontic status was analysed using multiple logistic regression. Multiple linear regression was used to analyse the association between prosthodontic status and nutritional intake.

RESULTS

The elderly subjects with partial or full dentures reported chewing difficulties 1.62-fold more frequently (95% CI: 1.06-2.49) than those with natural teeth or a fixed prosthesis after adjusting for gender, TMD (temporomandibular disorder), household income and education level. Additionally, daily nutritional intakes of energy, protein, fat, ash, calcium, phosphorus and thiamine were decreased significantly in elderly with partial or full dentures compared with those with no prosthesis or with a fixed prosthesis (P < 0.05).

CONCLUSIONS

Our findings underline oral health status and perceived disability in mastication are associated with dietary imbalances in the elderly. We suggest that the evaluation of patients' nutritional status should be considered as a part of an overall plan for dental hygiene care.

Search for top squarks in R-parity-violating supersymmetry using three or more leptons and b-tagged jets

A search for anomalous production of events with three or more isolated leptons and bottom-quark jets produced in pp collisions at √s=8 TeV is presented. The analysis is based on a data sample corresponding to an integrated luminosity of 19.5 fb(-1) collected by the CMS experiment at the LHC in 2012. No excess above the standard model expectations is observed. The results are interpreted in the context of supersymmetric models with signatures that have low missing transverse energy arising from light top-squark pair production with R-parity-violating decays of the lightest supersymmetric particle. In two models with different R-parity-violating couplings, top squarks are excluded below masses of 1020 GeV and 820 GeV when the lightest supersymmetric particle has a mass of 200 GeV.