The Folklore of Sorting Algorithms

The objective of this paper is to review the folklore knowledge seen in research work devoted on synthesis, optimization, and effectiveness of various sorting algorithms. We will examine sorting algorithms in the folklore lines and try to discover the tradeoffs between folklore and theorems. Finally, the folklore knowledge on complexity values of the sorting algorithms will be considered, verified and subsequently converged in to theorems

A Scalable VLSI Architecture for Soft-Input Soft-Output Depth-First Sphere Decoding

Multiple-input multiple-output (MIMO) wireless transmission imposes huge challenges on the design of efficient hardware architectures for iterative receivers. A major challenge is soft-input soft-output (SISO) MIMO demapping, often approached by sphere decoding (SD). In this paper, we introduce the - to our best knowledge - first VLSI architecture for SISO SD applying a single tree-search approach. Compared with a soft-output-only base architecture similar to the one proposed by Studer et al. in IEEE J-SAC 2008, the architectural modifications for soft input still allow a one-node-per-cycle execution. For a 4x4 16-QAM system, the area increases by 57% and the operating frequency degrades by 34% only.Comment: Accepted for IEEE Transactions on Circuits and Systems II Express Briefs, May 2010. This draft from April 2010 will not be updated any more. Please refer to IEEE Xplore for the final version. *) The final publication will appear with the modified title "A Scalable VLSI Architecture for Soft-Input Soft-Output Single Tree-Search Sphere Decoding

Technical Note: The Use of RNA-interference as a Tool to Find Proteins Involved in Melanosome Formation or Transport

Melanosomes are lysosome-related organelles that produce and transport the pigment melanin within melanocytes. Mutations in proteins required for melanosome transport and formation lead to a range of pigmentation defects, manifested at the cellular level as perinuclear clustering of melanosomes, or reduced sorting of melanosomal cargo such as tyrosinase-related protein 1 (TYRP1). A pilot screen was carried out to investigate whether a combination of cellular imaging and RNA interference could be used to identify new proteins involved in pigmentation pathways. In this study, eleven genes known to play a role in melanosome transport/formation or other pigmentation properties were knocked down in mouse melanocytes with shRNAmir constructs. The investigated genes were TYRP1, pallidin, cappuccino, dysbindin, HPS5, LYST, Myosin Va, melanophilin, RhoA, UBPY and mahogunin. In a blinded confocal imaging experiment, the only reproducible change observed in cells in which these targets were knocked down was a decrease in TYRP1 levels upon transfection with knockdown constructs against TYRP1 itself, or one of three constructs targeting HPS5 (Hermansky-Pudlak Syndrome 5). Upon analysis with high-content imaging software, only the knockdown construct against TYRP1 itself was detected. RT-PCR analysis showed that many of the shRNAmir constructs did not reduce mRNA and proteins levels enough to detect effects on melanosome properties. This was further examined for melanophilin, a protein necessary for melanosome transport. Altogether, the data show that this system is currently not sensitive enough for use in a screen for unknown regulators of melanosome transport and formation. The main obstacle appears to be incomplete reduction of target protein levels. Our observation that a ~50% reduction in mRNA level is not sufficient to elicit an effect is supported by the fact that heterozygous carriers of melanosomal transport disorders (Griscelli Syndrome, Hermansky-Pudlak Syndrome) do not display diseases phenotypes. A further reduction in protein levels, for example by viral infection of shRNA, may be required

Parallel String Sample Sort

We discuss how string sorting algorithms can be parallelized on modern multi-core shared memory machines. As a synthesis of the best sequential string sorting algorithms and successful parallel sorting algorithms for atomic objects, we propose string sample sort. The algorithm makes effective use of the memory hierarchy, uses additional word level parallelism, and largely avoids branch mispredictions. Additionally, we parallelize variants of multikey quicksort and radix sort that are also useful in certain situations.Comment: 34 pages, 7 figures and 12 table

Engineering Parallel String Sorting

We discuss how string sorting algorithms can be parallelized on modern multi-core shared memory machines. As a synthesis of the best sequential string sorting algorithms and successful parallel sorting algorithms for atomic objects, we first propose string sample sort. The algorithm makes effective use of the memory hierarchy, uses additional word level parallelism, and largely avoids branch mispredictions. Then we focus on NUMA architectures, and develop parallel multiway LCP-merge and -mergesort to reduce the number of random memory accesses to remote nodes. Additionally, we parallelize variants of multikey quicksort and radix sort that are also useful in certain situations. Comprehensive experiments on five current multi-core platforms are then reported and discussed. The experiments show that our implementations scale very well on real-world inputs and modern machines.Comment: 46 pages, extension of "Parallel String Sample Sort" arXiv:1305.115

Rapid creation and quantitative monitoring of high coverage shRNA libraries.

Short hairpin RNA libraries are limited by low efficacy of many shRNAs and by off-target effects, which give rise to false negatives and false positives, respectively. Here we present a strategy for rapidly creating expanded shRNA pools (approximately 30 shRNAs per gene) that are analyzed by deep sequencing (EXPAND). This approach enables identification of multiple effective target-specific shRNAs from a complex pool, allowing a rigorous statistical evaluation of true hits