An algorithm for computing the restriction scaffold assignment problem in computational biology

Let S and T be two finite sets of points on the real line with |S|+|T|=n and |S|>|T|. The restriction scaffold assignment problem in computational biology assigns each point of S to a point of T such that the sum of all the assignment costs is minimized, with the constraint that every element of T must be assigned at least one element of S. The cost of assigning an element si of S to an element tj of T is |si−tj|, i.e., the distance between si and tj. In 2003 Ben-Dor, Karp, Schwikowski and Shamir [J. Comput. Biol. 10 (2) (2003) 385] published an O(nlogn) time algorithm for this problem. Here we provide a counterexample to their algorithm and present a new algorithm that runs in O(n²) time, improving the best previous complexity of O(n³).     

Apparatus and initial results for pressurized planar electrochromatography

Pressurized planar electrochromatography (PPEC) is a new planar chromatographic technique in which the mobile phase is driven by electroosmotic flow, while the sorbent layer is pressurized in a manner that allows heat to flow from the layer through an electrically insulating, thermally conducting, sheet of aluminum nitride ceramic. A prototype apparatus for performing PPEC is described. Separation by PPEC is faster than by conventional TLC, and an example is presented of a 24-fold enhancement in the speed of separation. PPEC was performed on both regular and high-performance C18 layers, and the latter yield substantially faster separation. The sorbent layer requires conditioning at elevated temperature before use, and solute migration velocity increases with this temperature. The flow rate increases in a linear manner with increasing voltage and diminishes in a nonlinear manner with increasing pressure. Both electrical current and Joule heating diminish with increasing pressure, and the diminution of flow at high pressure can be compensated by an increase in voltage. PPEC is more efficient than classical TLC. Theoretical plate heights diminish with increasing Rf and are in the range 29-21 and 55-27 microm for the high-performance and regular plates, respectively. PPEC retains the advantages of classical TLC but has the ability to separate a substantially higher number of samples simultaneously. An example is presented on the separation of nine samples in 1 min on a 2.5 cm x 10 cm sorbent layer.     

Laser action from two dipyrrinone dyes under flash-lamp pumping

Two quasi-aromatic compounds, namely, two dipyrrinone dyes (Xanthoglow and Kryptoglow), exhibited strong fluorescence. Therefore they were tested for laser action under flash-lamp pumping. These two dyes outperformed Coumarin 540A and exhibited a high degree of photostability when dissolved in 1,4-dioxane. However, in all other solvents used, considerable photodecomposition was observed.     

Thermal dissociation of multimeric protein complexes by using nanoelectrospray mass spectrometry

The behavior of macromolecular systems at different temperatures is often crucial to their biological activity and function. While heat-induced changes of individual proteins are readily monitored by a number of spectroscopic methods, changes in noncovalent complexes of biomolecules are more challenging to interpret. Nanoelectrospray mass spectrometry is becoming increasingly powerful in the study of large noncovalent complexes, and here we describe the design, characterization, and application of a novel probe that allows the thermocontrol of the solution in the electrospray capillary. The transition temperature for the unfolding of the protein lysozyme is readily obtained and correlates closely with that measured by fluorescence spectroscopy, thereby demonstrating the validity of this approach. We apply this technique to the study of the 200-kDa complex of the small heat shock protein TaHSP16.9, revealing both its dissociation into suboligomeric species and an increase in its size and polydispersity at elevated temperatures. In contrast, gas-phase activation of this complex is also carried out and yields a dissociation pathway fundamentally different from that observed for thermal activation in solution. As such, this probe allows the study of the reversible heat-induced changes of noncovalent complexes in a biologically relevant manner.     

Premorbid anomalies and risk of schizophrenia and depressive disorders in a birth cohort exposed to prenatal rubella.

In a birth cohort prenatally exposed to rubella, we assessed whether prospectively documented premorbid neuromotor dysfunction, mannerisms, deviant behaviors, and temperament during childhood and adolescence were impaired in cases who developed depressive disorder (DD) relative to rubella-exposed controls and cases who developed schizophrenia spectrum psychosis (SSP). Premorbid neuromotor dysfunction and mannerisms were not increased among DD cases compared to controls or SSP cases. With regard to temperament, approachability was greater in DD cases than in controls and SSP cases. There were numerical increases in the proportions of DD cases with premorbid deviant behaviors compared to controls, but the findings fell short of statistical significance; the proportion of subjects with deviant behaviors in DD cases was similar to that found for SSP. These results indicate that premorbid neuromotor dysfunction and mannerisms may be specific to SSP among major psychiatric disorders in this cohort, and suggest that premorbid deviant behaviors are increased in both DD and SSP. Greater premorbid approachability may be associated with an increased risk of adult DD. Implications of these findings for school psychology are furnished. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The formation of an apatite coating on carboxylated polyphosphazenes via a biomimetic process

The biomimetic deposition of an apatite coating on polyphosphazene was investigated. A polyphosphazene having carboxylatophenoxy side groups was synthesized as a candidate polymer with heterogeneous nucleation sites for apatite deposition. Poly[bis(carboxylatophenoxy)phosphazene] (PCPP) was synthesized by a two-step synthetic route involving the synthesis of poly(dichlorophosphazene) (PDP) followed by nucleophilic replacement of the chlorine atoms of PDP with carboxylatophenoxy groups. The surface of the carboxylated polyphosphazene induced the formation of a dense layer of apatite on the surface after incubation in simulated body fluid at 37 °C with an ionic concentration approximately the same as that of human blood plasma. The results suggested an early precipitation of octacalcium phosphate and calcium phosphate intermediates on the surface, both of which are known to promote osteoblast differentiation and proliferation.     

More IMPATIENT: A gridding-accelerated Toeplitz-based strategy for non-Cartesian high-resolution 3D MRI on GPUs

Several recent methods have been proposed to obtain significant speed-ups in MRI image reconstruction by leveraging the computational power of GPUs. Previously, we implemented a GPU-based image reconstruction technique called the Illinois Massively Parallel Acquisition Toolkit for Image reconstruction with ENhanced Throughput in MRI (IMPATIENT MRI) for reconstructing data collected along arbitrary 3D trajectories. In this paper, we improve IMPATIENT by removing computational bottlenecks by using a gridding approach to accelerate the computation of various data structures needed by the previous routine. Further, we enhance the routine with capabilities for off-resonance correction and multi-sensor parallel imaging reconstruction. Through implementation of optimized gridding into our iterative reconstruction scheme, speed-ups of more than a factor of 200 are provided in the improved GPU implementation compared to the previous accelerated GPU code.     

James H. Fetzer,Philosophy and Cognitive Science,Second Edition: Revised and Expanded,Paragon Issues in Philosophy

Minds and Machines -     

Design and performance evaluation of swirl injectors for water evaporation at low pressure

This paper describes the design and performance evaluation of swirl injectors which find application in the spray flash desalination system at low pressures and temperatures. Water was sprayed into the vaporizer through a swirl injector as fine droplets. The vaporizer was maintained at low pressure. The maximum flow rate was 1 l/s. The injector performance was determined at different feed water temperatures, vacuum and water injection pressures. The effects of injector dimensions and flow parameters on droplet production were studied and analyzed. Droplet size of 0.7–0.9 mm from the theory compared with the experiments estimates. From this study, it is established that the droplet diameter in the range of 0.7–0.9 mm is optimum for flashing.     

MnS doped mesoporous silica catalysts for the generation of novel carbon nanocages

Novel MnS impregnated mesoporous silica systems have been originated for the generation of carbon nanocages. The procedure involves a simple catalytic vapour deposition (CVD) method. This is the first time that a transition metal sulfide has been used for the synthesis of carbon nanostructures.