High-Throughput Sequencing of Phage Display Libraries Reveals Parasitic Enrichment of Indel Mutants Caused by Amplification Bias

The combination of phage display technology with high-throughput sequencing enables in-depth analysis of library diversity and selection-driven dynamics. We applied short-read sequencing of the mutagenized region on focused display libraries of two homologous nucleic acid modification eraser proteins—AlkB and FTO—biopanned against methylated DNA. This revealed enriched genotypes with small indels and concomitant doubtful amino acid motifs within the FTO library. Nanopore sequencing of the entire display vector showed additional enrichment of large deletions overlooked by region-specific sequencing, and further impacted the interpretation of the obtained amino acid motifs. We could attribute enrichment of these corrupted clones to amplification bias due to arduous FTO display slowing down host cell growth as well as phage production. This amplification bias appeared to be stronger than affinity-based target selection. Recommendations are provided for proper sequence analysis of phage display data, which can improve motive discovery in libraries of proteins that are difficult to display.     

Progressive spatial processing deficits in a mouse model of the fragile X premutation.

Fragile X associated tremor/ataxia syndrome (FXTAS) is a neurodegenerative disorder that is the result of a CGG trinucleotide repeat expansion in the range of 55–200 in the 5′ UTR of the FMR1 gene. To better understand the progression of this disorder, a knock-in (CGG KI) mouse was developed by substituting the mouse CGG8 trinucleotide repeat with an expanded CGG98 repeat from human origin. It has been shown that this mouse shows deficits on the water maze at 52 weeks of age. In the present study, this CGG KI mouse model of FXTAS was tested on behavioral tasks that emphasize spatial information processing. The results demonstrate that at 12 and 24 weeks of age, CGG KI mice were unable to detect a change in the distance between two objects (metric task), but showed intact detection of a transposition of the objects (topological task). At 48 weeks of age, CGG KI mice were unable to detect either change in object location. These data indicate that hippocampal-dependent impairments in spatial processing may occur prior to parietal cortex-dependent impairments in FXTAS. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A simple and efficient parallel FFT algorithm using the BSP model

We present a new parallel radix-4 FFT algorithm based on the BSP model. Our parallel algorithm uses the group-cyclic distribution family, which makes it simple to understand and easy to implement. We show how to reduce the communication cost of the algorithm by a factor of 3, in the case that the input/output vector is in the cyclic distribution. We also show how to reduce computation time on computers with a cache-based architecture. We present performance results on a Cray T3E with up to 64 processors, obtaining reasonable efficiency levels for local problem sizes as small as 256 and very good efficiency levels for local sizes larger than 2048.     

Ten Ideas for Policymakers to Drive Digital Progress

Innovators continue to find new ways to use information technology (IT) to make our lives better. And looking forward, IT will continue to be a critical component of solutions to many social challenges. But policymakers must create the right environment for technological progress. This article offers ten guiding principals to create technology policy that spurs and sustains digital progress.     

选择低价FPGA开发板付出的高昂代价

在电子产品设计行业，随着FPGA等可编程器件的兴起，一向举止明智的企业开始有点失常。他们竟不对成本与效果、长期影响与工作流程效率进行综合而全面的考虑，仅着眼于短期效益，便对FPGA开发硬件与工具匆匆做出选择。     

Speed Scaling of Tasks with Precedence Constraints

We consider the problem of speed scaling to conserve energy in a multiprocessor setting where there are precedence constraints between tasks, and where the performance measure is the makespan. That is, we consider an energy bounded version of the classic problem Pm | prec | C _max. We extend the standard 3-field notation and denote this problem as Sm | prec, energy | C _max. We show that, without loss of generality, one need only consider constant power schedules. We then show how to reduce this problem to the problem Qm | prec | C _max to obtain a poly-log(m)-approximation algorithm. A preliminary version of this paper appears in Proceedings of the 3rd Workshop on Approximation and Online Algorithms (WAOA 2005). Research of K. Pruhs supported in part by NSF grants CCR-0098752, ANI-0123705, CNS-0325353, CCF-0448196, CCF-0514058, and IIS-0534531. Research of R. van Stee supported by Alexander von Humboldt-Stiftung.     

Public spaces, social planning and crime prevention

This paper provides a discussion of issues relating to public places, urban planning and community crime prevention. It explores the application of crime prevention approaches and techniques to the planning and management of public places, and provides examples of innovative practices and strategic planning processes. The paper then outlines a social mapping exercise which focuses on the physical, social and regulatory environments.     

Non-Discriminatory Automatic Registration of Knock-On Train Delays

Incidents and waiting for train connections are registered by dispatchers as sources of train delays, but route and headway conflicts are not always clearly recognized. Moreover, traffic management and route setting are the primary task of dispatchers and signallers, whilst monitoring and incident registration is not allowed to take up too much of their time. This paper describes a tool that automatically and without discrimination identifies route conflicts and the train numbers involved. It is based on standard train describer and infrastructure messages recorded on the Dutch railway network. The logic of these messages is captured in a coloured Petri net (CPN) model on which a prototype tool for route conflict identification and estimation of knock-on delay has been developed.     

Does regulation stimulate productivity? The effect of air quality policies on the efficiency of US power plants

This research examines the effect of air quality regulations on the productivity of US power plants based on both economic and environmental outputs. Using data envelopment analysis (DEA) to estimate an efficiency measure incorporating both economic and environmental outcomes, we look at changes in efficiency in US power plants over an eleven-year time period (1994–2004) during which several different regulations were implemented for the control of nitrogen oxides (NO_x) and sulfur dioxide (SO₂). The paper then models how estimated efficiency behaves over time as a function of regulatory changes. Findings suggest mixed effects of regulations on power plant efficiency when pollution abatement and electricity generation are both included as outputs.