The Experts below are selected from a list of 2061 Experts worldwide ranked by ideXlab platform
Daehyuk Kim - One of the best experts on this subject based on the ideXlab platform.
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global dna methylation in the chestnut blight fungus cryphonectria parasitica and genome wide changes in dna methylation accompanied with Sectorization
Frontiers in Plant Science, 2018Co-Authors: Jeesun Chun, Jyotiranjan Bal, Junhyun Jeon, Jungmi Kim, Jaeyoung Choi, Yonghwan Lee, Jin Hoe Huh, Daehyuk KimAbstract:Mutation in CpBck1, an ortholog of the cell wall integrity mitogen-activated protein kinase kinase kinase (MAPKKK) of Saccharomyces cerevisiae, in the chestnut blight fungus Cryphonectria parasitica resulted in a sporadic Sectorization as culture proceeded. The progeny from the sectored area maintained the characteristics of the sector, showing a massive morphogenetic change, including robust mycelial growth without differentiation. Epigenetic changes were investigated as the genetic mechanism underlying this Sectorization. Quantification of DNA methylation and whole-genome bisulfite sequencing revealed genome-wide DNA methylation of the wild-type at each nucleotide level and changes in DNA methylation of the sectored progeny. Compared to the wild-type, the sectored progeny exhibited marked genome-wide DNA hypomethylation but increased methylation sites. Expression analysis of two DNA methyltransferases, including two representative types of DNA methyltransferase (DNMTase), demonstrated that both were significantly down-regulated in the sectored progeny. However, functional analysis using mutant phenotypes of corresponding DNMTases demonstrated that a mutant of CpDmt1, an ortholog of RID of Neurospora crassa, resulted in the sectored phenotype but the CpDmt2 mutant did not, suggesting that the genetic basis of fungal Sectorization is more complex. The present study revealed that a mutation in a signaling pathway component resulted in Sectorization accompanied with changes in genome-wide DNA methylation, which suggests that this signal transduction pathway is important for epigenetic control of Sectorization via regulation of genes involved in DNA methylation.
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a mutant of the bck1 homolog from cryphonectria parasitica resulted in Sectorization with an impaired pathogenicity
Molecular Plant-microbe Interactions, 2016Co-Authors: Jungmi Kim, Joonggi Lee, Sukhyun Yun, Young Ho Kim, Seungmoon Park, Daehyuk KimAbstract:CpBck1, an ortholog of the cell-wall integrity mitogen-activated protein kinase kinase kinase of Saccharomyces cerevisiae, was cloned and characterized from the chestnut blight fungus Cryphonectria parasitica. The CpBck1-null mutant displayed cell wall integrity–related phenotypic changes such as abnormal cell morphology and wall formation and hypersensitivity to cell wall-disrupting agents. In addition, the mutant showed severely retarded growth without any sign of normal development, such as hyphal differentiation, conidiation, or pigmentation. As the culture proceeded, the mutant colony showed sporadic Sectorization. Once sectored, the sectored phenotype of robust mycelial growth without differentiation was stably inherited. Compared with the wild type, both the parental CpBck1-null mutant and the sectored progeny exhibited marked impaired virulence. The present study revealed that a mutation in a signaling pathway component related to cell-wall integrity resulted in sporadic Sectorization and these se...
Victor H Alcoceryamanaka - One of the best experts on this subject based on the ideXlab platform.
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dual use value of network partitioning for water system management and protection from malicious contamination
Journal of Hydroinformatics, 2015Co-Authors: Armando Di Nardo, Michele Di Natale, Giovanni Francesco Santonastaso, Velitchko Tzatchkov, Dino Musmarra, Victor H AlcoceryamanakaAbstract:This paper considers the introduction of a contaminant into a water supply system using a backflow attack. The recent development of techniques for water network Sectorization, aimed at improving the management of water systems, is also an efficient way to protect networks from intentional contamination and to reduce the risk of the dangerous effects of network contamination. Users can be significantly protected by isolated district meter areas (i-DMAs) in the water network and the closing of the gate valves by a remote control system to implement such i-DMAs in cases of malicious attacks. This study investigates the effects of different approaches for water network partitioning and Sectorization to protect networks using a technique for designing i-DMAs that is compatible with hydraulic performance and that is based on graph theory and heuristic optimization. For this analysis, the introduction of cyanide through a backflow attack was assumed. The methodology was tested on a large water network in Mexico and displayed good protection from a malicious attack.
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water network Sectorization based on graph theory and energy performance indices
Journal of Water Resources Planning and Management, 2014Co-Authors: Armando Di Nardo, Michele Di Natale, Giovanni Francesco Santonastaso, Velitchko Tzatchkov, Victor H AlcoceryamanakaAbstract:AbstractThis paper proposes a new methodology for the optimal design of water network Sectorization, which is an essential technique for improving the management and security of multiple-source water supply systems. In particular, the network Sectorization problem under consideration concerns the definition of isolated district meter areas, each of which is supplied by its own source (or sources) and is completely disconnected from the rest of the water system through boundary valves or permanent pipe sectioning. The proposed methodology uses graph theory principles and a heuristic procedure based on minimizing the amount of dissipated power in the water network. The procedure has been tested on two existing water distribution networks (WDNs) (in Parete, Italy and San Luis Rio Colorado, Mexico) using different performance indices. The simulation results, which confirmed the effectiveness of the proposed methodology, surpass empirical trial-and-error approaches and offer water utilities a tool for the desi...
Saman Amarasinghe - One of the best experts on this subject based on the ideXlab platform.
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compiler 2 0 using machine learning to modernize compiler technology
Languages Compilers and Tools for Embedded Systems, 2020Co-Authors: Saman AmarasingheAbstract:Modern compilers are still built using technology that existed decades ago. These include basic algorithms and techniques for lexing, parsing, data-flow analysis, data dependence analysis, vectorization, register allocation, instruction selection, and instruction scheduling. It is high time that we modernize our compiler toolchain. In this talk, I will show the path to the modernization of one important compiler technique -- vectorization. Vectorization was first introduced in the era of Cray vector processors during the 1980's. In modernizing vectorization, I will first show how to use new techniques that better target modern hardware. While vector supercomputers need large vectors, which are only available by parallelizing loops, modern SIMD instructions efficiently work on short vectors. Thus, in 2000, we introduced Superword Level Parallelism (SLP) based vectorization. SLP finds short vector instructions within basic blocks, and by loop unrolling we can convert vector parallelism to SLP. Next, I will show how we can take advantage of the power of modern computers for compilation, by using more accurate but expensive techniques to improve SLP vectorization. Due to the hardware resource constraints of the era, like many other compiler optimizations, SLP implementation was a greedy algorithm. In 2018, we introduced goSLP, which uses integer linear programming to find an optimal instruction packing strategy and achieves 7.58% geomean performance improvement over the LLVM's SLP implementation on SPEC2017fp C/C++ programs. Finally, I will show how to truly modernize a compiler by automatically learning the necessary components of the compiler with Ithemal and Vemal. The optimality of goSLP is under LLVM's simple per instruction additive cost model that fits within the Integer programming framework. However, the actual cost of execution in a modern out-of-order, pipelined, superscalar processor is much more complex. Manually building such cost models as well as manually developing compiler optimizations is costly, tedious, error-prone and is hard to keep up with the architectural changes. Ithemal is the first learnt cost model for predicting the throughput of x86 basic blocks. It not only significantly outperforms (more than halves the error) state-of-the-art analytical hand-written tools like llvm-mca, but also is learnt from data requiring minimal human effort. Vemal is a learnt policy for end-to-end vectorization as opposed to tuning heuristics, which outperforms LLVM's SLP vectorizer. These data-driven techniques can help achieve state-of-the-art results while also reducing the development and maintenance burden of the compiler developer.
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goSLP: Globally Optimized Superword Level Parallelism Framework
Proceedings of the ACM on Programming Languages, 2018Co-Authors: Charith Mendis, Saman AmarasingheAbstract:Modern microprocessors are equipped with single instruction multiple data (SIMD) or vector instruction sets which allow compilers to exploit superword level parallelism (SLP), a type of fine-grained parallelism. Current SLP auto-vectorization techniques use heuristics to discover vectorization opportunities in high-level language code. These heuristics are fragile, local and typically only present one vectorization strategy that is either accepted or rejected by a cost model. We present goSLP, a novel SLP auto-vectorization framework which solves the statement packing problem in a pairwise optimal manner. Using an integer linear programming (ILP) solver, goSLP searches the entire space of statement packing opportunities for a whole function at a time, while limiting total compilation time to a few minutes. Furthermore, goSLP optimally solves the vector permutation selection problem using dynamic programming. We implemented goSLP in the LLVM compiler infrastructure, achieving a geometric mean speedup of 7.58% on SPEC2017fp, 2.42% on SPEC2006fp and 4.07% on NAS benchmarks compared to LLVM's existing SLP auto-vectorizer.
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exploiting vector parallelism in software pipelined loops
International Symposium on Microarchitecture, 2005Co-Authors: Samuel Larsen, Rodric Rabbah, Saman AmarasingheAbstract:An emerging trend in processor design is the addition of short vector instructions to general-purpose and embedded ISAs. Frequently, these extensions are employed using traditional vectorization technology first developed for supercomputers. In contrast, scalar hardware is typically targeted using ILP techniques such as software pipelining. This paper presents a novel approach for exploiting vector parallelism in software pipelined loops. The proposed methodology. Our approach results in better resource utilization and allows for software pipelining with shorter initiation intervals. The proposed optimization is applied in the compiler backend, where vectorization decisions are more amenable to cost analysis. This is unique in that traditional vectorization optimizations are usually carried out at the statement level. Although our technique most naturally complements statically scheduled machines, we believe it is applicable to any architecture that tightly integrates support for instruction and data level parallelism. We evaluate our methodology using nine SPEC FP benchmarks. In comparison to software pipelining, our approach achieves a maximum speedup of 1.38x, with average of 1.11x
And Gil R Hawley - One of the best experts on this subject based on the ideXlab platform.
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crystallization melting and morphology of syndiotactic polypropylene fractions 4 in situ lamellar single crystal growth and melting in different sectors
Macromolecules, 2000Co-Authors: Wensheng Zhou, Stephen Z D Cheng, Sirina Putthanarat, Darrell H Reneker, Bernard Lotz, Sergei Magonov, Eric T Hsieh, Rolf G Geerts, Syriac J Palackal, And Gil R HawleyAbstract:Over a wide crystallization temperature (Tc) range, elongated rectangular lamellar single crystals of syndiotactic polypropylene (s-PP) grown from the melt of thin films exhibit Sectorization along both diagonal directions to form the (010) [with the (010) free edge] and the (100) [with the (100) free edge] sectors. They can be observed by transmission electron and atomic force microscopy (TEM and AFM). Electron diffraction experiments show that the crystals in both sectors are form III orthorhombic structure, as recently proposed.1-4 The observation of this Sectorization is due to the thickness difference between these two sectors with different fold planes. In situ observations of the single-crystal growth are monitored using an AFM coupled with a hot stage. The Tc-dependent crystal growth rates along both the (100) and (010) normal can be measured, and they are anisotropic. This leads to a large aspect ratio of the rectangular single crystal. AFM results also show that the thickness difference between ...
Guowei Wang - One of the best experts on this subject based on the ideXlab platform.
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prediction of dendrite orientation and stray grain distribution in laser surface melted single crystal superalloy
Journal of Materials Science & Technology, 2017Co-Authors: Guowei Wang, Jingjing Liang, Yizhou Zhou, Zhuangqi HuAbstract:A vectorization analysis technique for crystal growth and microstructure development in single-crystal weld was developed in our previous work. Based on the vectorization method, crystal growth and stray grain distribution in laser surface remelting of single crystal superalloy CMSX-4 were investigated in combination of simulations with experimental observations. The energy distribution of laser was taken into consideration in this research. The experimental results demonstrate that the simulation model applies well in the prediction of dendrite growth direction. Moreover, the prediction of stray grain distribution works well except for the region of dendrites growing along the [100] direction.
