| 1. |
- Kanayama, Kengo, et al.
(författare)
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Genome-wide mapping of bivalent histone modifications in hepatic stem/progenitor cells
- 2019
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Ingår i: Stem Cells International. - : Hindawi Limited. - 1687-966X .- 1687-9678. ; 2019
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Tidskriftsartikel (refereegranskat)abstract
- The “bivalent domain,” a distinctive histone modification signature, is characterized by repressive trimethylation of histone H3 at lysine 27 (H3K27me3) and active trimethylation of histone H3 at lysine 4 (H3K4me3) marks. Maintenance and dynamic resolution of these histone marks play important roles in regulating differentiation processes in various stem cell systems. However, little is known regarding their roles in hepatic stem/progenitor cells. In the present study, we conducted the chromatin immunoprecipitation (ChIP) assay followed by high-throughput DNA sequencing (ChIP-seq) analyses in purified delta-like 1 protein (Dlk + ) hepatic stem/progenitor cells and successfully identified 562 genes exhibiting bivalent domains within 2 kb of the transcription start site. Gene ontology analysis revealed that these genes were enriched in developmental functions and differentiation processes. Microarray analyses indicated that many of these genes exhibited derepression after differentiation toward hepatocyte and cholangiocyte lineages. Among these, 72 genes, including Cdkn2a and Sox4, were significantly upregulated after differentiation toward hepatocyte or cholangiocyte lineages. Knockdown of Sox4 in Dlk + cells suppressed colony propagation and resulted in increased numbers of albumin + /cytokeratin 7 + progenitor cells in colonies. These findings implicate that derepression of Sox4 expression is required to induce normal differentiation processes. In conclusion, combined ChIP-seq and microarray analyses successfully identified bivalent genes. Functional analyses of these genes will help elucidate the epigenetic machinery underlying the terminal differentiation of hepatic stem/progenitor cells.
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| 2. |
- Amer, Abdelhalim, et al.
(författare)
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Scaling FMM with data-driven OpenMP tasks on multicore architectures
- 2016
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Ingår i: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - Cham : Springer International Publishing. - 1611-3349 .- 0302-9743. ; 9903 LNCS, s. 156-170
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Tidskriftsartikel (refereegranskat)abstract
- Poor scalability on parallel architectures can be attributed to several factors, among which idle times, data movement, and runtime overhead are predominant. Conventional parallel loops and nested parallelism have proved successful for regular computational patterns. For more complex and irregular cases, however, these methods often perform poorly because they consider only a subset of these costs. Although data-driven methods are gaining popularity for efficiently utilizing computational cores, their data movement and runtime costs can be prohibitive for highly dynamic and irregular algorithms, such as fast multipole methods (FMMs). Furthermore, loop tiling, a technique that promotes data locality and has been successful for regular parallel methods, has received little attention in the context of dynamic and irregular parallelism. We present a method to exploit loop tiling in data-driven parallel methods. Here, we specify a methodology to spawn work units characterized by a high data locality potential. Work units operate on tiled computational patterns and serve as building blocks in an OpenMP task-based data-driven execution. In particular, by the adjusting work unit granularity, idle times and runtime overheads are also taken into account. We apply this method to a popular FMM implementation and show that, with careful tuning, the new method outperforms existing parallel-loop and user-level thread-based implementations by up to fourfold on 48 cores.
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| 3. |
- Rademacher, Georg, et al.
(författare)
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159 Tbit/s C+L Band Transmission over 1045 km 3-Mode Graded-Index Few-Mode Fiber
- 2018
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Ingår i: 2018 Optical Fiber Communications Conference and Exposition, OFC 2018 - Proceedings.
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Konferensbidrag (refereegranskat)abstract
- We transmit 3 x348 x 24.5 Gbaud PDM-16-QAM modulated C+L band channels with a total data-rate of over 159 Tbit/s over 1045 km graded-index three-mode fiber, resulting in a record throughput-distance product of more than 166 Pbit/sxkm.
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| 4. |
- Unat, Didem, et al.
(författare)
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Trends in Data Locality Abstractions for HPC Systems
- 2017
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Ingår i: IEEE Transactions on Parallel and Distributed Systems. - : IEEE Computer Society. - 1045-9219 .- 1558-2183. ; 28:10, s. 3007-3020
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Tidskriftsartikel (refereegranskat)abstract
- The cost of data movement has always been an important concern in high performance computing (HPC) systems. It has now become the dominant factor in terms of both energy consumption and performance. Support for expression of data locality has been explored in the past, but those efforts have had only modest success in being adopted in HPC applications for various reasons. them However, with the increasing complexity of the memory hierarchy and higher parallelism in emerging HPC systems, locality management has acquired a new urgency. Developers can no longer limit themselves to low-level solutions and ignore the potential for productivity and performance portability obtained by using locality abstractions. Fortunately, the trend emerging in recent literature on the topic alleviates many of the concerns that got in the way of their adoption by application developers. Data locality abstractions are available in the forms of libraries, data structures, languages and runtime systems; a common theme is increasing productivity without sacrificing performance. This paper examines these trends and identifies commonalities that can combine various locality concepts to develop a comprehensive approach to expressing and managing data locality on future large-scale high-performance computing systems.
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