Radial clustergrams: visualizing the aggregate properties of hierarchical clusters

A new radial space-filling method for visualizing cluster hierarchies is presented. The method, referred to as a radial clustergram, arranges the clusters into a series of layers, each representing a different level of the tree. It uses adjacency of nodes instead of links to represent parent-child relationships and allocates sufficient screen real estate to each node to allow effective visualization of cluster properties through color-coding. Radial clustergrams combine the most appealing features of other cluster visualization techniques but avoid their pitfalls. Compared to classical dendrograms and hyperbolic trees, they make much more efficient use of space; compared to treemaps, they are more effective in conveying hierarchical structure and displaying properties of nodes higher in the tree. A fisheye lens is used to focus on areas of interest, without losing sight of the global context. The utility of the method is demonstrated using examples from the fields of molecular diversity and conformational analysis.     

Isotactic polyethylenimines induce formation of L-amino acids in transamination

Isotactic polyethylenimines with (S)-benzyl side chains were synthesized from 4-(S)-4-benzyl-2-oxazolines. When alpha-keto acids were subjected to transamination in the presence of this polymer, and a pyridoxamine coenzyme modified with hydrophobic chains, enantioselectivity toward the natural isomer (l > d) was observed, followed by racemization of the amino acid products. However, the racemization did not occur when the coenzyme was covalently attached to the polymer. [reaction: see text]     

Multilevel Deep Feature Generation Framework for Automated Detection of Retinal Abnormalities Using OCT Images

Optical coherence tomography (OCT) images coupled with many learning techniques have been developed to diagnose retinal disorders. This work aims to develop a novel framework for extracting deep features from 18 pre-trained convolutional neural networks (CNN) and to attain high performance using OCT images. In this work, we have developed a new framework for automated detection of retinal disorders using transfer learning. This model consists of three phases: deep fused and multilevel feature extraction, using 18 pre-trained networks and tent maximal pooling, feature selection with ReliefF, and classification using the optimized classifier. The novelty of this proposed framework is the feature generation using widely used CNNs and to select the most suitable features for classification. The extracted features using our proposed intelligent feature extractor are fed to iterative ReliefF (IRF) to automatically select the best feature vector. The quadratic support vector machine (QSVM) is utilized as a classifier in this work. We have developed our model using two public OCT image datasets, and they are named database 1 (DB1) and database 2 (DB2). The proposed framework can attain 97.40% and 100% classification accuracies using the two OCT datasets, DB1 and DB2, respectively. These results illustrate the success of our model.     

Enhancement of Jc by Hf-doping in the superconductor MgB2: A hyperfine interaction study

Measurements of the critical current density (J_c) by magnetisation and the upper critical field (H_c2) by magnetoresistance have been performed for hafnium-doped MgB₂. There has been a remarkable enhancement of J_c as compared to that by ion irradiation without any appreciable decrease in T_c, which is beneficial from the point of view of applications. The irreversibility line extracted from J_c shows an upward shift. In addition, there has been an increase in the upper critical field which indicates that Hf partially substitutes for Mg. Hyperfine interaction parameters obtained from time differential perturbed angular correlation (TDPAC) measurements revealed the formation of HfB and HfB₂ phases along with the substitution of Hf. A possible explanation is given for the role of these species in the enhancement of J_c in MgB₂ superconductor.     

Effect of unfolding on the thickness of the hydration layer of a protein

Properties of water in the hydration layer around a protein is intimately correlated with its function. A knowledge of the thickness of the hydration layer is important to understand its role in guiding the folding-unfolding of the protein. We have performed atomistic molecular dynamics simulations of the folded native and a partially unfolded molten globule structure of the villin headpiece subdomain or HP-36 in aqueous solution to estimate the effect of unfolding on the thickness of hydration layer around different segments of the protein. In particular, several dynamic properties of water around different segments of the folded native and the unfolded structure have been calculated by varying the thickness of the hydration layers. It is found that unfolding of a segment of the protein is correlated with the dynamics of water around it, i.e., within the first hydration layer. The effect of unfolding on water properties has been found to diminish when water molecules present beyond the first hydration layer were included in the calculations.      

Laser surface modification of Al–4Cu–1Mg alloy for enhanced thermal conductivity

The feasibility of enhancing thermal conductivity of Al–4Cu–1Mg alloy by depositing 80Cu–20Mo coating using high-power lasers has been examined. Coatings of 667±2.5 μm thickness were formed with metallurgically sound interface. Results showed an 86% increase in the thermal conductivity of Al–4Cu–1Mg alloy due to laser-deposited 80Cu–20Mo alloy coating. This coating approach can potentially be used on low coefficient of thermal expansion metal matrix composites to enhance their thermal conductivity in electronic devices.     

In situ generation of palladium oxide nano-crystals

Synthesis of metal–organic framework (MOF) based on tetra-pyridyl porphyrin and palladium (II) salt resulted in the formation of palladium oxide nano-crystals. The palladium oxide nano-crystals were characterized by PXRD, TEM, HRTEM, ED, UV–Vis spectroscopy, DLS, SEM and AFM. A plausible mechanism for the in situ generation of nano-crystals has been proposed.     

Strong CH⋅⋅⋅Halide Hydrogen Bonds from 1,2,3‐Triazoles Quantified Using Pre‐Organized and Shape‐Persistent Triazolophanes

The structures associated with halide (F^?, Cl^?, Br^?) complexation inside CH hydrogen‐bonding macrocyclic receptors, called triazolophanes, are characterized using density functional theory (DFT). The associated binding energies in the gas and solution phases are evaluated. The ruffles in the empty triazolophane become smoothed‐out upon Cl^?‐ and Br^?‐ion binding directly into the middle of the cavity. The largely pre‐organized cavity morphs into an elliptical shape to facilitate shorter hydrogen bonds in the north and south regions and longer ones west and east. The smaller F^? ion sits in, and flattens‐out, only the north (or south) region. The 1,2,3‐triazoles show shorter CH???Cl^? contacts than for the phenylenes. Both Cl^? and Br^? show the same binding geometries but Cl^? has a larger binding energy consistent with its stronger Lewis basicity. Model triads were used to decompose the overall binding energy into those of its components. In the course of this triad analysis, anion polarization was identified and its contribution to the triad???Cl^? binding energy estimated. Consequently, the binding energies for the individual aryl units within the comparatively non‐polarized triazolophanes were estimated. The 1,2,3‐triazoles are twice as strong as the phenylenes thus contributing most of the interaction energy to Cl^?‐ion binding. Therefore, the 1,2,3‐triazoles appear to approach the hydrogen bond strengths of the NH donors of pyrrole units.     

Dynamical analysis of toxin producing Phytoplankton–Zooplankton interactions

In the present paper we consider a toxin producing phytoplankton–zooplankton model in which the toxin liberation by phytoplankton species follows a discrete time variation. Firstly we consider the elementary dynamical properties of the toxic-phytoplankton–zooplankton interacting model system in absence of time delay. Then we establish the existence of local Hopf-bifurcation as the time delay crosses a threshold value and also prove the existence of stability switching phenomena. Explicit results are derived for stability and direction of the bifurcating periodic orbit by using normal form theory and center manifold arguments. Global existence of periodic orbits is also established by using a global Hopf-bifurcation theorem. Finally, the basic outcomes are mentioned along with numerical results to provide some support to the analytical findings.     

Structure of poly(propyl ether imine) dendrimer from fully atomistic molecular dynamics simulation and by small angle x-ray scattering

We study the structure of carboxylic acid terminated neutral poly(propyl ether imine) (PETIM) dendrimer from generations 1-6 (G1-G6) in a good solvent (water) by fully atomistic molecular dynamics (MD) simulations. We determine as a function of generation the structural properties such as radius of gyration, shape tensor, asphericity, fractal dimension, monomer density distribution, and end-group distribution functions. The sizes obtained from the MD simulations have been validated by small angle x-ray scattering experiment on dendrimer of generations 2-4 (G2-G4). A good agreement between the experimental and theoretical value of radius of gyration has been observed. We find a linear increase in radius of gyration with the generation. In contrast, Rg scales as approximately Nx with the number of monomers. We find two distinct exponents depending on the generations, x=0.47 for G1-G3 and x=0.28 for G3-G6, which reveal their nonspace filling nature. In comparison with the amine terminated poly(amidoamine) (PAMAM) dendrimer, we find that Rg of Gth generation PETIM dendrimer is nearly equal to that of (G+1)th generation of PAMAM dendrimer as observed by Maiti et al. [Macromolecules 38, 979 (2005)]. We find substantial back folding of the outer subgenerations into the interior of the dendrimer. Due to their highly flexible nature of the repeating branch units, the shape of the PETIM dendrimer deviates significantly from the spherical shape and the molecules become more and more spherical as the generation increases. The interior of the dendrimer is quite open with internal cavities available for accommodating guest molecules, suggesting the use of PETIM dendrimer for guest-host applications. We also give a quantitative measure of the number of water molecules present inside the dendrimer.