GlyNet: a multi-task neural network for predicting protein–glycan interactions

Advances in diagnostics, therapeutics, vaccines, transfusion, and organ transplantation build on a fundamental understanding of glycan–protein interactions. To aid this, we developed GlyNet, a model that accurately predicts interactions (relative binding strengths) between mammalian glycans and 352 glycan-binding proteins, many at multiple concentrations. For each glycan input, our model produces 1257 outputs, each representing the relative interaction strength between the input glycan and a particular protein sample. GlyNet learns these continuous values using relative fluorescence units (RFUs) measured on 599 glycans in the Consortium for Functional Glycomics glycan arrays and extrapolates these to RFUs from additional, untested glycans. GlyNet''s output of continuous values provides more detailed results than the standard binary classification models. After incorporating a simple threshold to transform such continuous outputs the resulting GlyNet classifier outperforms those standard classifiers. GlyNet is the first multi-output regression model for predicting protein–glycan interactions and serves as an important benchmark, facilitating development of quantitative computational glycobiology.

GlyNet, a neural net model of glycan-protein binding strengths. Given a glycan it outputs binding to each of several protein samples. Reproducing glycan array data, it extrapolates the binding of untested glycans against the protein samples.     

Infrared and microwave spectra, molecular conformation and electric dipole moment of methyl thiolformate

The microwave spectrum (41-10 GHz) and the infrared spectrum (4000-50 cm⁻¹) of methyl thiolformate have been obtained and analyzed. The spectra are consistent with a single molecular conformation having a planar array of heavy atoms and with the alkyl group cis to the carbonyl group. The measured rotational constants are: A, 11042.22 MHz; B, 5118.27 MHz; C, 3562.03 MHz (κ = −0.5839). No internal rotation doublets were observed in the microwave spectrum for the ground vibrational state, which implies that the barrier hindering internal rotation of the methyl group is either much larger or much smaller than the corresponding value for methyl formate. If the former is true then a lower limit of 10.5 kJ mol⁻¹ may be placed on the barrier height.The dipole moment of methyl thiolformate was measured using the Stark effect to be 1.58 ± 0.05 Debyes (μ_A = 1.52 D; μ_B = 0.43 D) for the vapor, and for dilute solutions in benzene at 295 K the value of 1.6 ± 0.1 D was found from capacitance measurements.SCF computations using minimal basis sets of STO/3G atomic orbitals and extended basis sets of STO/4.31G atomic orbitals have been carried out for methyl thiolformate and methyl formate. Energy differences between rotational isomers and estimates of barrier heights are given together with the calculated dipole moments.     

Angular dependence of the dipole-dipole interaction in a nearly one-dimensional sample of Rydberg atoms

Atoms in an ultracold highly excited sample are strongly coupled through the dipole-dipole interaction. In an effort to understand and manipulate the complicated interactions in this system we are investigating their dependence on the relative orientation of the dipoles. By focusing a 480 nm beam from a tunable dye laser into a magneto-optical trap, we produce a nearly one-dimensional sample of Rydberg atoms. The trap lies at the center of four conducting rods with which we can vary the magnitude and direction of the electric field at the trap, thus controlling the orientation of the dipoles with respect to the sample axis. We have measured the strength of the interaction for a variety of relative orientations.     

Entropy-stabilized smectic C phase in a system of zigzag-shaped molecules

We report Monte Carlo simulations of a system of rigid zigzag-shaped molecules that demonstrate that simple excluded-volume interactions are sufficient to produce a fluid tilted lamellar [smectic C (SmC)] liquid crystal phase. The molecules are composed of three rigidly linked hard spherocylinders arranged in a zigzag fashion. By varying the zigzag angle we have mapped out the whole phase diagram as a function of pressure and zigzag angle Psi. For Psi between 35 degrees and 80 degrees our model simulation exhibits the SmC phase. This is the first conclusive evidence where steric interactions arising out of molecular shape alone induce the occurrence of the SmC phase for a wide range of zigzag angles. For smaller Psi, a transition from tilted crystal to crystal is observed.     

Lagrange solution for three wavelength solitary wave clusters in nematic liquid crystals

We investigate the interaction of three optical solitary waves propagating with angular momentum in bulk nematic liquid crystals. The resulting cluster of solitary waves, or nematicons, is shown to orbit about its common centre of “mass”. An elongated isosceles triangle configuration is derived, this solution being the equivalent of the Lagrange solution of Newtonian gravitation. This triangle solution is found to be stable owing to diffractive radiation. A modulation theory explains the existence of the triangle solution as due to the non-monotonicity of an effective potential for the interaction of the solitary waves. This modulation theory also gives good agreement with numerical solutions for the trajectories of the nematicons in the three colours. Finally, it is shown that a cut-off in the shed diffractive radiation prevents the break-up of the triangle due to radiative losses.     

Phase-shifting interferometry with four interferograms using linear polarization modulation and a Ronchi grating displaced by only a small unknown amount

A method to reduce the number of captures needed in phase-shifting interferometry is proposed on the basis of grating interferometry and modulation of linear polarization. The case of four interferograms is considered. A common-path interferometer is used with two windows in the object plane and a Ronchi grating as the pupil, thus forming several replicated images of each window over the image plane. The replicated images, under proper matching conditions, superpose in such a way so that they produce interference patterns. Orders 0 and +1 and −1 and 0 form useful patterns to extract the optical phase differences associated to the windows. A phase of π is introduced between these orders using linear polarizing filters placed in the windows and also in the replicated windows, so two π-shifted patterns can be captured in one shot. An unknown translation is then applied to the grating in order to produce another shift in the each pattern. A second and final shot captures these last patterns. The actual grating displacement and the phase shift can be determined according to the method proposed by Kreis before applying proper phase-shifting techniques to finally calculate the phase difference distribution between windows. Related simulations and experimental results are given.     

Semiconductor optical fibres: progress and opportunities

This paper reviews recent progress in the nascent field of semiconductor optical fibres, from the fundamentals through to device demonstration. The incorporation of semiconductor materials into both the step‐index and microstructured fibre geometries provides a route to introducing new optoelectronic functionality into existing glass fibre technologies. Herein, the various fabrication methods that have been developed as of to date are described, and their compatibility with the different semiconductor materials and fibre designs discussed. Results will be presented on the optical transmission properties of several fibre types, with particular attention being paid to the observation of nonlinear propagation in silicon core fibres. Finally, some speculation regarding the future prospects and applications of this new class of fibre will be provided.     

Combined effects of pressure and temperature on enzyme stability

Abstract

The effect of high temperature and high hydrostatic pressure on the residual hydrolytic activity of a commercial Rhizomucor miehei lipase has been studied. Inactivation at high temperature and/or high pressure was carried out. Under non-denaturing pressure conditions, results showed that pressurisation protects enzymes against thermal deactivation. This is in accordance with previous results obtained with enzymes from mesophilic sources, such as invertase and galactosidases.