Physicochemical Methods for Prediction of Functional Information for Proteins

Structural genomics initiatives are determining thousands of new protein structures. Many of these structures are of unknown function, and computational methods for the rapid determination of functional information from protein structure are needed. We present details of how functional information is obtained from the structure using THEMATICS (Theoretical Microscopic Titration Curves). THEMATICS is a computational procedure that gives information about chemical reactivity, based on solution of the Poisson-Boltzmann equations for the electrical potential function. We show how anomalies in predicted titration curves are established. We show further that when residues with anomalous predicted titration curves form a cluster in physical space, these residues tend to be very highly conserved across species and such clusters are reliable predictors of the active site. Results are given for ten enzymes; detailed results are shown for the enzymes triosephosphate isomerase (from chicken), 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (from E. coli), and papain (from papaya).     

Encapsulation and controlled release in polyacrylamide hydrogels

A novel host–guest system was developed by the encapsulation of simple organic guest molecules in the hydrophilic molecular architecture of crosslinked polyacrylamide hydrogels. The crosslinking agents used for the preparation of the host systems were hexanediol dimethacrylate (HDDMA) and divinyl benzene (DVB). This enabled us to construct hydrogels with different hydrophobic–hydrophilic equilibria. The model guest system used for the studies was benzoic acid. The selections gave simple but excellent host–guest systems with fine polar–apolar balancing. Polyacrylamide hydrogels with encapsulated benzoic acid were prepared with varying crosslink densities (5, 10, 15, and 20 mol %) by the solution polymerization technique. The rate of release of the host from the host–guest assembly was studied in different swelling conditions. The rate of release depended on the interaction forces between the polymer and the solvents. Polar forces, dispersion forces, and hydrogen bonding all played a vital role. The swelling behavior of the host‐polymer system and the host–guest assembly was analyzed and compared by the Flory–Rehner method. The amount of benzoic acid encapsulated in the DVB‐crosslinked polymer was higher than in the HDDMA‐crosslinked polymer, and the rate of release was in the order 5 > 15 > 10 > 20% for the DVB‐crosslinked polymer. The rate of release for the HDDMA‐crosslinked host–guest assembly was in the order 10 > 5 > 15 > 20%. These results were in excellent agreement with those of the Flory–Rehner analysis of the swelling properties. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 93: 1816–1824, 2004     

Simulation of carbon nanotube based p-n junction diodes

Taking advantage of the unique characteristics of an ambipolar carbon nanotube field effect transistor (CNTFET), a ‘p-n junction’ is simulated along the single-walled carbon nanotube channel using two separate gates close to the source and drain of the CNTFET, respectively. The current-voltage characteristics of the double-gated CNTFET are calculated using a semiclassical method based on the Schottky barrier field effect transistor mechanism. The calculation results show a good rectification performance of the p-n junction.     

Residual encoder-decoder up-sampling for structural preservation in noise removal

Multimedia Tools and Applications - While denoising 3D MRI, structural preservation is a very critical process in the medical region. However, Rician noise in MRI has affected the image quality...     

Glycated proteome: From reaction to intervention

Glycation, a nonenzymatic reaction between reducing sugars and proteins, is a proteome wide phenomenon, predominantly observed in diabetes due to hyperglycemia. Glycated proteome of plasma, kidney, lens, and brain are implicated in the pathogenesis of various diseases, including diabetic complications, neurodegenerative diseases, cancer, and aging. This review discusses the strategies to characterize protein glycation, its functional implications in different diseases, and intervention strategies to protect the deleterious effects of protein glycation.     

Gestural systems for the voice: performance approaches and repertoire

ABSTRACT

Singing, like dance, emerges directly from the body. The voice, in combination with whole body movement, constitutes a potent form of self-expression. Gestural systems offer a specialized context in which to explore the intersection between voice and movement. The practice-based investigation presented in this article charts the development of an original musical work, Intangible Spaces, which gives form to the invisible aspects of voice and movement through gestural control, physical modelling synthesis and visual feedback. I draw on embodied and performative autoethnographic methods to capture the felt sensations and sound-movement associations that arise during the composition process. I also explore the performance approaches of key practitioners in the area to gain a broader understanding of the ways in which musicians leverage existing performance skills to uncover novel connections between movement and voice in gestural performance.     

Evaluation of Reorientation Techniques and Distractors for Walking in Large Virtual Environments

Vir tual Environments (VEs) that use a real-walking locomotion interface have typically been restricted in size to the area of the tracked lab space. Techniques proposed to lift this size constraint, enabling real walking in VEs that are larger than the tracked lab space, all require reorientation techniques (ROTs) in the worst-case situation—when a user is close to walking out of the tracked space. We propose a new ROT using visual and audial distractors—objects in the VE that the user focuses on while the VE rotates—and compare our method to current ROTs through three user studies. ROTs using distractors were preferred and ranked more natural by users. Our findings also suggest that improving visual realism and adding sound increased a user's feeling of presence. Users were also less aware of the rotating VE when ROTs with distractors were used.     

Aberrant protein expression in plasma and kidney tissue during experimental obstructive nephropathy

Kidney failure is a major health problem worldwide. Patients with end-stage renal disease require intensive medical support by dialysis or kidney transplantation. Current methods for diagnosis of kidney disease are either invasive or insensitive, and renal function may decline by as much as 50% before it can be detected using current techniques. The goal of this study was, therefore, to identify biomarkers of kidney disease (associated with renal fibrosis) that can be used for the development of a non-invasive clinical test for early disease detection. We utilized two protein-profiling technologies (SELDI-TOF MS and 2-D) to screen the plasma and kidney proteome for aberrantly expressed proteins in an experimental mouse model of unilateral uretric obstruction, which mimics the pathology of human renal disease. Several differentially regulated proteins were detected at the plasma level of day-3-obstructed animals, which included serum amyloid A1, fibrinogen α, haptoglobin precursor protein, haptoglobin and major urinary proteins 11 and 8. Differentially expressed proteins detected at the tissue level included ras-like activator protein 2, haptoglobin precursor protein, malate dehydrogenase, α enolase and murine urinary protein (all p<0.05 versus controls). Immunohistochemistry was used to confirm the up-regulation of fibrinogen. Interestingly, these proteins are largely separated into four major classes: (i) acute-phase reactants (ii) cell-signaling molecules (iii) molecules involved in cell growth and metabolism and (iv) urinary proteins. These results provide new insights into the pathology of obstructive nephropathy and may facilitate the development of specific assay(s) to detect and monitor renal fibrosis.     

Design and Development of Flexible PDMS Antenna for UWB-WBAN Applications

Wireless Personal Communications - This paper presents the design and development of a flexible Ultra Wide Band (UWB) antenna using polydimethylsiloxane as a substrate. Copper foil having a...