Hybrid continuum–coarse-grained modeling of erythrocytes

The red blood cell (RBC) membrane is a composite structure, consisting of a phospholipid bilayer and an underlying membrane-associated cytoskeleton. Both continuum and particle-based coarse-grained RBC models make use of a set of vertices connected by edges to represent the RBC membrane, which can be seen as a triangular surface mesh for the former and a spring network for the latter. Here, we present a modeling approach combining an existing continuum vesicle model with a coarse-grained model for the cytoskeleton. Compared to other two-component approaches, our method relies on only one mesh, representing the cytoskeleton, whose velocity in the tangential direction of the membrane may be different from that of the lipid bilayer. The finitely extensible nonlinear elastic (FENE) spring force law in combination with a repulsive force defined as a power function (POW), called FENE–POW, is used to describe the elastic properties of the RBC membrane. The mechanical interaction between the lipid bilayer and the cytoskeleton is explicitly computed and incorporated into the vesicle model. Our model includes the fundamental mechanical properties of the RBC membrane, namely fluidity and bending rigidity of the lipid bilayer, and shear elasticity of the cytoskeleton while maintaining surface-area and volume conservation constraint. We present three simulation examples to demonstrate the effectiveness of this hybrid continuum–coarse-grained model for the study of RBCs in fluid flows.     

Finite-Time Destruction of Entanglement and Non-Locality by Environmental Influences

Entanglement and non-locality are non-classical global characteristics of quantum states important to the foundations of quantum mechanics. Recent investigations have shown that environmental noise, even when it is entirely local in influence, can destroy both of these properties in finite time despite giving rise to full quantum state decoherence only in the infinite time limit. These investigations, which have been carried out in a range of theoretical and experimental situations, are reviewed here.     

Shamrock surfactants with terminal carboxylate headgroups and a central phosphorodithioate or quaternary ammonium headgroup

Surfactants 3 (tripotassium O,O'-di-[11-(carboxylato)undecyl]phosphorodithioate) and 4 (sodium 12-[dimethyl-(11-carboxylatoundecyl)ammonio]dodecanoate), which are new shamrock surfactants, were prepared and characterized. Shamrock surfactants represent a novel class of surfactants that contain a central headgroup connected to two flanking headgroups by hydrocarbon chains; they do not contain long-chain alkyl groups. Surfactants 3 and 4 were characterized in water by measurement of their Krafft temperatures and critical aggregation concentrations, and their aggregates were studied by 1H and 31P NMR spectroscopy, dynamic laser light scattering, and phase-contrast optical microscopy. Aqueous 3 and 4 were also studied by cryoetch high-resolution scanning electron microscopy, which revealed fences with interposed lacelike patterns for the former and compartments formed by irregular fences for the latter. Coacervates were likely formed upon the undisturbed hydration of 3 and 4, as determined by phase-contrast optical microscopy.     

On the Identification of the Parts of Compound Quantum Objects

A view of the constitution of quantum objects as reducible, in the sense of being decomposable to elementary particles, is outlined. On this view, parts of composite quantum systems are considered to be identified according to a recently introduced, specifically quantum notion of individuation (Jaeger, Found Phys 40:1396 2010). These parts can typically also be considered particles according to Wigner’s symmetry-based notion. Particles are considered elementary when they satisfy a condition of elementarity, newly introduced here, that improves on that provided by Newton and Wigner. In any given instance, the compound character of a physical object can be verified in principle by decomposition, ultimately to a set of such elementary parts, through appropriate precise quantum measurements during experimentation consistently with this principle of individuation.     

Validity and Reliability of the Reflux Symptom Index (RSI)

Laryngopharyngeal reflux (LPR) is present in up to 50% of patients with voice disorders. Currently, there is no validated instrument that documents symptom severity in LPR. We developed the reflux symptom index (RSI), a self-administered nine-item outcomes instrument for LPR. The purpose of this investigation was to evaluate the psychometric properties of the RSI. For validity assessment, 25 patients with LPR were evaluated prospectively before and six months after b.i.d. treatment with proton pump inhibitors (PPI). Each patient completed the RSI as well as the 30-item voice handicap index (VHI). For reliability assessment, the study patients were given the RSI on two separate occasions before the initiation of treatment. Normative RSI data were derived from 25 age-matched and gender-matched controls taken from an existing database of asymptomatic individuals without any evidence of LPR. The mean RSI (+/- standard deviation) of patients with LPR improved from 21.2 (+/- 10.7) to 12.8 (+/- 10.0), and the mean VHI improved from 52.2 (+/- 24.7) to 41.5 (+/- 25.0) after 6 months of therapy (p = 0.001 and 0.065, respectively). Of the three VHI subscales (emotional, physical, functional), only the functional subscale improved significantly (p = 0.037). Patients who experienced a five point or better improvement in RSI were 11 times more likely to experience a five-point improvement in VHI (95% confidence interval = 1.7, 76.8). For reliability assessment, the first and second pretreatment RSIs were 19.9 (+/- 11.1) and 20.9 (+/- 9.6), respectively (correlation coefficient = 0.81, p < 0.001). The single-item correlation coefficients ranged from 0.41 to 0.91 (p < 0.05 for all items). The mean pretreatment RSI in patients with LPR was significantly higher than controls (21.2 versus 11.6; p < 0.001). The mean RSI of patients with LPR after 6 months of PPI therapy approached that of asymptomatic controls (p > 0.05). The RSI is easily administered, highly reproducible, and exhibits excellent construct and criterion-based validity.     

Fibronectin: An Interesting Vocal Fold Protein

A great deal of information is accruing regarding the function of the extracellular matrix. Once thought to be simply a structural entity to surround cells, it is now known to do much more. Fibronectin in particular has received specific attention. Fibronectin is a ubiquitous glycoprotein found most abundantly in the extracellular matrix of regenerating, healing, and embryonic tissue. Vast evidence supports the fact that fibronectin participates in many diverse functions throughout the body that are relevant to vocal fold biology. This article introduces the structure of fibronectin and its isoforms and provides an introduction to some of the many functions it plays. It also reviews the evidence about fibronectin's place in vocal folds and vocal fold pathology. It discusses fibronectin's presence in vocal nodules, vocal polyps, vocal scarring, and Reinke's edema, and reviews the data on its role in mucosal wave impairment. Lastly, it discusses preliminary microarray data that show gene expression for fibronectin to be upregulated in true vocal folds when compared to false vocal folds.     

Short-Term Therapeutic Trial of Proton Pump Inhibitors in Suspected Extraesophageal Reflux

Pharyngoesophageal gastric acid reflux is thought to initiate chronic posterior laryngitis. The gold standard for measuring gastric reflux is dual-channel 24-hour pH monitoring. This is a time-consuming, inconvenient, expensive method that is not available in all areas. New therapeutic regimes that make use of proton pump inhibitors (PPIs) have proven to be therapeutically efficient for control of acid reflux. Twenty-four consecutive patients with chronic voice disorders and signs of posterior laryngitis were selected for therapy. Twenty-four hour pH monitoring was performed independently before the therapy. The trial therapy consisted of all patients receiving pantoprazole, 40 mg once daily for 6 weeks. Immediately following the therapy a statistically significant (p < 0.05) improvement was observed in all patients. This improvement was analyzed retrospectively by comparison with the results of 24-hour pH monitoring. In 71% of the patients the 24-hour pH-monitoring gave a positive result showing a high number of patients with extraesophageal reflux in our study group. Patients with positive results of pH-monitoring responded in a statistically significant manner (p < 0.05) to the pantoprazole therapy, whereas those patients without detected reflux did not. A 3-month follow-up of the patients with a positive result of the pH-monitoring confirmed the improvement. No patients reported adverse effects. A 6-week treatment with pantoprazole can be clinically justified. It helps to save time and reduce costs, allows for selection of reflux-negative patients for alternative therapy, and may prevent inadequate treatment of patients with false-negative pH monitoring. Twenty-four hour pH monitoring is still recommended for patients unresponsive to this trial therapy.     

Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme's pathway

Mutations in DNA polymerase β (pol β) have been associated with approximately 30% of human tumors. The E295K mutation of pol β has been linked to gastric carcinoma via interference with base excision repair. To interpret the different behavior of E295K as compared to wild-type pol β in atomic and energetic detail, we resolve a binary crystal complex of E295K at 2.5 ? and apply transition path sampling (TPS) to delineate the closing pathway of the E295K pol β mutant. Conformational changes are important components in the enzymatic pathway that lead to and ready the enzyme for the chemical reaction. Our analyses show that the closing pathway of E295K mutant differs from the wild-type pol β in terms of the individual transition states along the pathway, associated energies, and the active site conformation in the final closed form of the mutant. In particular, the closed state of E295K has a more distorted active site than the active site in the wild-type pol β. In addition, the total energy barrier in the conformational closing pathway is 65 ± 11 kJ/mol, much higher than that estimated for both correct (e.g., G:C) and incorrect (e.g., G:A) wild-type pol β systems (42 ± 8 and 45 ± 7 kJ/mol, respectively). In particular, the rotation of Arg258 is the rate-limiting step in the conformational pathway of E295K due to unfavorable electrostatic and steric interactions. The distorted active site in the closed relative to open state and the high energy barrier in the conformational pathway may explain in part why the E295K mutant is observed to be inactive. Interestingly, however, following the closing of the thumb but prior to the rotation of Arg258, the E295K mutant complex has a similar energy level as compared to the wild-type pol β. This suggests that the E295K mutant may associate with DNA with similar affinity, but it may be hampered in continuing the process of chemistry. Supporting experimental data come from the observation that the catalytic activity of wild-type pol β is hampered when E295K is present: this may arise from the competition between E295K and wild-type enzyme for the DNA. These combined results suggest that the low insertion efficiency of E295K mutant as compared to wild-type pol β may be related to a closed form distorted by unfavorable electrostatic and steric interactions between Arg258 and other key residues. The active site is thus less competent for proceeding to the chemical reaction, which may also involve a higher reaction barrier than the wild-type or may not be possible in this mutant. Our analysis also suggests further experiments for other mutants to test the above hypothesis and dissect the roles of steric and electrostatic factors on enzyme behavior.