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).     

平台2015:Intel处理器及平台在下一个十年的演化

毫无疑问,近年来计算技术取得了长足的进步。但是,在未来的十年,主流计算技术中新的工作量、使用模式的出现及变化对未来的计算平台提出的要求,与过去十年所取得的进展也差不多,这些巨大的要求包括:更高的性能、更低的功率密度、更好的功能可扩展性。倘若出现这些使用计算机的震撼性的变化,我们怎样定义和构架未来的计算平台,就将不得不做出引人注目的改变。要整体地理解和满足的,不仅仅有计算的需要,而且还有接口以及系统基础设施的需要。Intel对这三个基础平台要素的演化的长期设想,以及驱动演化的架构的创新和核心能力,即是我们称之为平台2015(Platform2015)的内容。除了考察相关的趋势、使用、平台处理含意之外,本文将集中在平台2015的计算单元,描述Intel微处理器架构在未来十年的演化。     

Long-Term Dynamic Modeling Approach to Quantifying Attached Algal Growth and Associated Impacts on Dissolved Oxygen in the Lower Truckee River, Nevada

Nutrient loads enter the lower Truckee River of western Nevada, affecting the growth of attached algae (periphyton) which causes depressed nighttime dissolved oxygen (DO) levels. The lower Truckee River is home to the endangered cui-ui and threatened Lahontan cut-throat trout, with DO standards being established to in part protect these species. Hydrodynamics, nutrient concentrations, periphyton biomass, and DO data spanning August 2000–December 2001 were used to calibrate and verify a modified version of the Water Quality Analysis Simulation Program Version 5 (WASP5). Under typical loading conditions the periphyton community is nitrogen limited, however nitrogen loading from an upstream wastewater treatment facility increased greatly during the analysis period due to approved site construction activities (discharge permit excursion) causing the periphyton community to temporarily become phosphorus limited. The developed modeling approach, with limited calibration, was able to accurately track dynamic system responses. Removing the impact of the noted discharge permit excursion resulted in a minimum computed DO value of 4.13?mg/L, occurring at the downstream end of the modeling domain on August 8, 2001. Additionally removing the impact of all nutrient loads from area agriculture resulted in a predicted minimum DO value of 4.54?mg/L, while also shifting its location significantly upstream and its timing to April 26, 2001. Meeting all prescribed DO standards required establishing a minimum in-stream flow value of 1.81?m3/s (64.0?ft3/s) downstream of Derby Dam.     

Ascertaining the importance of neurons to develop better brain-machine interfaces

In the design of brain-machine interface (BMI) algorithms, the activity of hundreds of chronically recorded neurons is used to reconstruct a variety of kinematic variables. A significant problem introduced with the use of neural ensemble inputs for model building is the explosion in the number of free parameters. Large models not only affect model generalization but also put a computational burden on computing an optimal solution especially when the goal is to implement the BMI in low-power, portable hardware. In this paper, three methods are presented to quantitatively rate the importance of neurons in neural to motor mapping, using single neuron correlation analysis, sensitivity analysis through a vector linear model, and a model-independent cellular directional tuning analysis for comparisons purpose. Although, the rankings are not identical, up to sixty percent of the top 10 ranking cells were in common. This set can then be used to determine a reduced-order model whose performance is similar to that of the ensemble. It is further shown that by pruning the initial ensemble neural input with the ranked importance of cells, a reduced sets of cells (between 40 and 80, depending upon the methods) can be found that exceed the BMI performance levels of the full ensemble.     

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.     

Ein neues destillationsverfahren zur meerwasserentsalung nach dem regenerativprinzip

The process described here is based on the principle of regeneration according to which the heat of condensation of the fresh water produced is retained in a regenerator within a given temperature range and used for the repeated evaporation of further amounts of water. The periodicity and reversibility of heating and cooling periods of the regenerator is brought about by means of an external water circuit in a system of series-connected chambers forming a cascade. The temperature in the said chambers changing periodically with regard to time and place. Conventional heat exchangers made of corrosion-resisting alloys are not required in this process. Regenerator and cascade can be constructed in a simple way.     

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.