K-means: Clustering by gradual data transformation

Traditional approach to clustering is to fit a model (partition or prototypes) for the given data. We propose a completely opposite approach by fitting the data into a given clustering model that is optimal for similar pathological data of equal size and dimensions. We then perform inverse transform from this pathological data back to the original data while refining the optimal clustering structure during the process. The key idea is that we do not need to find optimal global allocation of the prototypes. Instead, we only need to perform local fine-tuning of the clustering prototypes during the transformation in order to preserve the already optimal clustering structure.     

Probing Protein Folding with Sequence-Reversed α-Helical Bundles

Recurrent protein folding motifs include various types of helical bundles formed by α-helices that supercoil around each other. While specific patterns of amino acid residues (heptad repeats) characterize the highly versatile folding motif of four-α-helical bundles, the significance of the polypeptide chain directionality is not sufficiently understood, although it determines sequence patterns, helical dipoles, and other parameters for the folding and oligomerization processes of bundles. To investigate directionality aspects in sequence-structure relationships, we reversed the amino acid sequences of two well-characterized, highly regular four-α-helical bundle proteins and studied the folding, oligomerization, and structural properties of the retro-proteins, using Circular Dichroism Spectroscopy (CD), Size Exclusion Chromatography combined with Multi-Angle Laser Light Scattering (SEC-MALS), and Small Angle X-ray Scattering (SAXS). The comparison of the parent proteins with their retro-counterparts reveals that while the α-helical character of the parents is affected to varying degrees by sequence reversal, the folding states, oligomerization propensities, structural stabilities, and shapes of the new molecules strongly depend on the characteristics of the heptad repeat patterns. The highest similarities between parent and retro-proteins are associated with the presence of uninterrupted heptad patterns in helical bundles sequences.     

Poly[(N‐isopropylacrylamide)‐co‐(itaconic acid)] hydrogels with poly(ethylene glycol)

The aim of the work reported here was to investigate temperature‐ and pH‐sensitive hydrogels of N‐isopropylacrylamide (NIPAM) and itaconic acid (IA) and their semi‐interpenetrating polymer networks (semi‐IPNs) with varying contents of poly(ethylene glycol) (PEG). The stimuli responsiveness, swelling behaviour and mechanical properties of the hydrogels and semi‐IPNs were studied in order to investigate the effect of various amounts of PEG. Pulsed‐gradient spin‐echo NMR experiments were carried out to investigate the diffusion process. The pH sensitivity increased with an increasing amount of PEG in the semi‐IPNs, while the overall rate of water uptake was diffusion‐controlled (n < 0.5). For certain PEG contents (5 and 10 wt%), the semi‐IPNs exhibited better mechanical properties than the poly(NIPAM‐co‐IA) copolymer. The calculated values of the self‐diffusion coefficients of water indicated facilitated diffusion of water through the system with increased amounts of PEG, while the self‐diffusion coefficients of a model compound, metoprolol tartrate, showed no significant dependence on the amount of PEG. According to the results obtained and compared to results reported in the literature, the investigated semi‐IPNs may have potential applications in the controlled release of macromolecular active agents such as proteins and peptides. Copyright © 2009 Society of Chemical Industry     

Synthesis,characterization and application of poly(N-isopropylacrylamide-co-itaconic acid) hydrogels as supports for lipase immobilization

Temperature- and pH-sensitive hydrogels based on N-isopropylacrylamide (NiPAAm) and itaconic acid (IA) were applied for immobilization of lipase from Candida rugosa (CRL). The hydrogels were synthesized by free radical crosslinking copolymerization in the presence of lipase. Characterization of samples by swelling studies, at pH 2.20 and 6.80 at a temperature of 37 °C, scanning electron microscopy (SEM) and Fourier transform infrared analysis (FT-IR) confirmed that the degree of crosslinking, the non-ionic/ionic (NiPAAm/IA) ratio and the enzyme content had impacts on the hydrogel structure, mechanical properties, morphology and swelling kinetics. All hydrogels demonstrated protein loading efficiencies as high as 95 wt.%. A specific activity of the immobilized lipase of around 38 IU/g was attained for an enzyme loading of 20.0 wt.%. As a result, improved pH and temperature optima values were obtained for the immobilized systems in relation to those for the free lipase.     

Visual Change With Moving Displays: More Evidence for Color Feature Map Inhibition During Preview Search.

Preview search with moving stimuli was investigated. The stimuli moved in multiple directions, and preview items could change either their color or their shape before onset of the new (search) displays. In Experiments 1 and 2, the authors found that (a) a preview benefit occurred even when more than 5 moving items had to be ignored, and (b) color change, but not shape change, disrupted preview search in moving stimuli. In contrast, shape change, but not color change, disrupted preview search in static stimuli (Experiments 3 and 4). Results suggest that preview search with moving displays is influenced by inhibition of a color map, whereas preview search with static displays is influenced by inhibition of locations of old distractors. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A full-wave Helmholtz model for continuous-wave ultrasound transmission

A full-wave Helmholtz model of continuous-wave (CW) ultrasound fields may offer several attractive features over widely used partial-wave approximations. For example, many full-wave techniques can be easily adjusted for complex geometries, and multiple reflections of sound are automatically taken into account in the model. To date, however, the full-wave modeling of CW fields in general 3D geometries has been avoided due to the large computational cost associated with the numerical approximation of the Helmholtz equation. Recent developments in computing capacity together with improvements in finite element type modeling techniques are making possible wave simulations in 3D geometries which reach over tens of wavelengths. The aim of this study is to investigate the feasibility of a full-wave solution of the 3D Helmholtz equation for modeling of continuous-wave ultrasound fields in an inhomogeneous medium. The numerical approximation of the Helmholtz equation is computed using the ultraweak variational formulation (UWVF) method. In addition, an inverse problem technique is utilized to reconstruct the velocity distribution on the transducer which is used to model the sound source in the UWVF scheme. The modeling method is verified by comparing simulated and measured fields in the case of transmission of 531 kHz CW fields through layered plastic plates. The comparison shows a reasonable agreement between simulations and measurements at low angles of incidence but, due to mode conversion, the Helmholtz model becomes insufficient for simulating ultrasound fields in plates at large angles of incidence.     

Energy‐dependent effects of resveratrol in Saccharomyces cerevisiae

The metabolic effects induced by resveratrol have been associated mainly with the consumption of high‐calorie diets; however, its effects with standard or low‐calorie diets remain unclear. To better understand the interactions between resveratrol and cellular energy levels, we used Saccharomyces cerevisiae as a model. Herein it is shown that resveratrol: (a) decreased cell viability in an energy‐dependent manner; (b) lessening of cell viability occurred specifically when cells were under cellular respiration; and (c) inhibition of oxygen consumption in state 4 occurred at low and standard energy levels, whereas at high energy levels oxygen consumption was promoted. These findings indicate that the effects of resveratrol are dependent on the cellular energy status and linked to metabolic respiration. Importantly, our study also revealed that S. cerevisiae is a suitable and useful model to elucidate the molecular targets of resveratrol under different nutritional statuses. Copyright © 2016 John Wiley & Sons, Ltd.     

Modified bounded homotopies to enable a narrow bounding zone

The aim of this paper is to introduce modifications that enhance the usability of the bounded homotopy methods proposed by Paloschi [1995. Bounded homotopies to solve systems of algebraic nonlinear equations. Computers and Chemical Engineering 19, 1243-1254; 1997. Bounded homotopies to solve systems of sparse algebraic nonlinear equations. Computers and Chemical Engineering 21, 531-541], especially in the area of chemical engineering. In modified bounded homotopies, the homotopy path is tracked by exploiting mapped variables instead of unmapped ones. Path tracking based on mapped variables makes it significantly easier to track the bounded homotopy path even though the bounding zone has to be narrow. Mapping also improves the bounding effect of bounded homotopies and makes it possible to avoid unreasonable variable values in homotopy path tracking. The performance of the modifications is illustrated with test cases. These examples clearly show that the modifications enlarge the capability and accuracy of bounded homotopies when solving both small- and large-scale sets of nonlinear equations describing chemical engineering problems.