One-Step Generalized Estimating Equations With Large Cluster Sizes

Medical studies increasingly involve a large sample of independent clusters, where the cluster sizes are also large. Our motivating example from the 2010 Nationwide Inpatient Sample (NIS) has 8,001,068 patients and 1049 clusters, with average cluster size of 7627. Consistent parameter estimates can be obtained naively assuming independence, which are inefficient when the intra-cluster correlation (ICC) is high. Efficient generalized estimating equations (GEE) incorporate the ICC and sum all pairs of observations within a cluster when estimating the ICC. For the 2010 NIS, there are 92.6 billion pairs of observations, making summation of pairs computationally prohibitive. We propose a one-step GEE estimator that (1) matches the asymptotic efficiency of the fully iterated GEE; (2) uses a simpler formula to estimate the ICC that avoids summing over all pairs; and (3) completely avoids matrix multiplications and inversions. These three features make the proposed estimator much less computationally intensive, especially with large cluster sizes. A unique contribution of this article is that it expresses the GEE estimating equations incorporating the ICC as a simple sum of vectors and scalars.     

An Ant Colony Optimisation algorithm for solving the asymmetric traffic assignment problem

In this paper we propose an Ant Colony Optimisation (ACO) algorithm for defining the signal settings on urban networks following a local approach. This consists in optimising the signal settings of each intersection of an urban network as a function only of traffic flows at the accesses to the same intersection, taking account of the effects of signal settings on costs and on user route choices. This problem, also known as Local Optimisation of Signal Settings (LOSS), has been widely studied in the literature and can be formulated as an asymmetric assignment problem. The proposed ACO algorithm is based on two kinds of behaviour of artificial ants which allow the LOSS problem to be solved: traditional behaviour based on the response to pheromones for simulating user route choice, and innovative behaviour based on the pressure of an ant stream for solving the signal setting definition problem. Our results on real-scale networks show that the proposed approach allows the solution to be obtained in less time but with the same accuracy as in traditional MSA (Method of Successive Averages) approaches.     

Optimisation of sensor positions in random linear arrays based on statistical relations between geometry and performance

Due to the widespread use of acoustic arrays, optimisation techniques for array design, focused on improving array performance, have been widely published. This paper exploits the statistical relation between different measures of sidelobe levels and the spacing of elements in random linear arrays made up of a small number of sensors. This paper defines the methodology to obtain maximum probability functions, associating array geometry and performance. These maximum probability functions allow a pre-selection of those array geometries that are more likely to be associated to specified sidelobe level values. This pre-selection results in a significantly reduced computational burden.     

Simplified model for mass diffusivity estimation based on dynamic pendant drop volume analysis

We present a simplified correlation for calculating the dissolved gas moles in a pendant drop during the diffusion time, for several drop shapes. After this correlation is determined, the Yang and Gu (Ind Eng Chem Res 44:4474–4483, 2005) dynamic pendant drop volume analysis (DPDVA) method for calculation of mass diffusivity from the pendant drop volume variation against time can be used. We solved the differential equation in cylindrical coordinates for the mass transfer model of the gas diffusion into the liquid inside the pendant drop, using a different characteristic length (L_C), instead of the outer radius of the syringe needle (r_n) used in Yang and Gu (Ind Eng Chem Res 44:4474–4483, 2005) for defining the dimensionless variables. L_C is the relationship between the pendant drop volume and its mass transfer surface area at the initial conditions. The generalized correlation saves time, simplifies the method application and the deviations in the diffusion coefficient calculation respect to the complete Yang and Gu model are below 6%.     

A pH-Induced Reversible Conformational Switch Able to Control the Photocurrent Efficiency in a Peptide Supramolecular System

External stimuli are potent tools that Nature uses to control protein function and activity. For instance, during viral entry and exit, pH variations are known to trigger large protein conformational changes. In Nature, also the electron transfer (ET) properties of ET proteins are influenced by pH-induced conformational changes. In this work, a pH-controlled, reversible 3₁₀-helix to α-helix conversion (from acidic to highly basic pH values and vice versa) of a peptide supramolecular system built on a gold surface is described. The effect of pH on the ability of the peptide SAM to generate a photocurrent was investigated, with particular focus on the effect of the pH-induced conformational change on photocurrent efficiency. The films were characterized by electrochemical and spectroscopic techniques, and were found to be very stable over time, also in contact with a solution. They were also able to generate current under illumination, with an efficiency that is the highest recorded so far with biomolecular systems.     

Differences in Salivary Proteins as a Function of PROP Taster Status and Gender in Normal Weight and Obese Subjects

Taste plays an important role in processes such as food choices, nutrition status and health. Salivary proteins contribute to taste sensitivity. Taste reduction has been associated with obesity. Gender influences the obesity predisposition and the genetic ability to perceive the bitterness of 6-n-propylthiouracil (PROP), oral marker for food preferences and consumption. We investigated variations in the profile of salivary proteome, analyzed by HPLC-ESI-MS, between sixty-one normal weight subjects (NW) and fifty-seven subjects with obesity (OB), based on gender and PROP sensitivity. Results showed variations of taste-related salivary proteins between NW and OB, which were differently associated with gender and PROP sensitivity. High levels of Ps-1, II-2 and IB-1 proteins belonging to basic proline rich proteins (bPRPs) and PRP-1 protein belonging to acid proline rich proteins (aPRPs) were found in OB males, who showed a lower body mass index (BMI) than OB females. High levels of Ps-1 protein and Cystatin SN (Cyst SN) were found in OB non-tasters, who had lower BMI than OB super-tasters. These new insights on the role of salivary proteins as a factor driving the specific weight gain of OB females and super-tasters, suggest the use of specific proteins as a strategic tool modifying taste responses related to eating behavior.     

Simultaneous Determination of Barbital and Thiobarbituric Acid by Derivative Spectrophotometry

A new method for the simultaneous determination of barbital and thiobarbituric acid by derivative spectrophotometry is proposed. The method allows the resolution of mixtures of the two components over the concentration ranges 0.37–4.70 μg/ml (barbital) and 0.40–4.50 μg/ml (thiobarbituric acid) provided the ratio between their concentrations does not exceed 5:1. It was applied to the determination of the two compounds in synthetic samples and blood serum.     

Unravelling the Time Scale of Conformational Plasticity and Allostery in Glycan Recognition by Human Galectin-1

The interaction of human galectin-1 with a variety of oligosaccharides, from di-(N-acetyllactosamine) to tetra-saccharides (blood B type-II antigen) has been scrutinized by using a combined approach of different NMR experiments, molecular dynamics (MD) simulations, and isothermal titration calorimetry. Ligand- and receptor-based NMR experiments assisted by computational methods allowed proposing three-dimensional structures for the different complexes, which explained the lack of enthalpy gain when increasing the chemical complexity of the glycan. Interestingly, and independently of the glycan ligand, the entropy term does not oppose the binding event, a rather unusual feature for protein-sugar interactions. CLEANEX-PM and relaxation dispersion experiments revealed that sugar binding affected residues far from the binding site and described significant changes in the dynamics of the protein. In particular, motions in the microsecond-millisecond timescale in residues at the protein dimer interface were identified in the presence of high affinity ligands. The dynamic process was further explored by extensive MD simulations, which provided additional support for the existence of allostery in glycan recognition by human galectin-1.     

Luminescent Graphene-Based Materials via Europium Complexation on Dipyridylpyridazine-Functionalized Graphene Sheets

Graphene-based materials exhibit outstanding physical properties and so are potentially applicable in a great variety of fields. Unlike their corresponding oxides, graphite and graphene are not prone to functionalization. Diels–Alder reactions are among the scarce reactions that they can occur without disrupting their conjugated sp² systems. Herein, the reaction between graphite and 3,6-di(2-pyridyl)-1,2,4,5-tetrazine under different conditions affords several graphene-based materials consisting of dipyridylpyridazine-functionalized few-layer graphene, multilayer graphene and graphite, the sheets of which act as ligands for the grafting of a europium complex. These three materials show strong red emission under 365 nm UV radiation. Their emitting particles can be visualized by confocal microscopy. The rich coordination chemistry of dipyridylpyridazine ligands has potential novel properties for similarly functionalized graphene-based materials grafted with other metal complexes.     

Poly(ionic liquid)s derived from 3‐octyl‐1‐vinylimidazolium bromide and N‐isopropylacrylamide with tunable properties

A new series of linear and crosslinked copolymers, obtained from 3‐octyl‐1‐vinylimidazolium bromide (VImBr) and N‐isopropylacrylamide (NIPAAm), were prepared by radical polymerization. Namely, VImBr was synthesized from 1‐bromooctane and an ionic liquid such as 1‐vinylimidazole. NIPAAm was used because it gives raise to well known thermoresponsive (co‐)polymers. The copolymers were thoroughly characterized by means of ¹H NMR and ¹³C NMR spectroscopies. Besides, differential scanning calorimetry, Fourier transform infrared spectroscopy, and scanning electron microscopy were also used. Moreover, the swelling behavior and the thermoresponsive properties of the corresponding hydrogels were studied. It was found that the VImBr incorporation into the copolymers does have a dramatic influence on both the thermal properties of the dried materials and the lower critical solution temperature of the corresponding hydrogels. In detail, the glass transition temperature was dependent on the monomer ratios, and ranged from 5 to 155 °C. Analogously, the lower critical solution temperature of the resulting hydrogels ranged from less than 10 up to 38 °C, thus including the physiological temperature. NMR spectroscopies, which were performed on the linear polymers, indicated that the monomers exhibit an alternating tendency resulting in a microstructure in which blocks are not present, at least when the two monomers are in equimolar amounts. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 3521–3532