471 research outputs found
Author Retrospective for Semantical Interprocedural Parallelization: An Overview of the PIPS Project
No full textInternational audienceThe PIPS project was started in 1988 to investigate the automatic detection of medium- and large-grain parallelism in scienti c programs thanks to summarization techniques based on convex array regions. By 1992 the PIPS system had reached its original goals, but it has morphed into a comprehensive, open-source platform still in use today. What were the key scienti c and engineering decisions that made this possible in spite of some inevitable shortcomings
A Simple Data Dependency Analyzer For C Programs.
No full textData dependencies that exist in a sequential program are a major hindrance towards parallelization
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Metabolic Regulation of Preimplantation Mouse Embryo Development
No full textPreimplantation mammalian embryo is a critical stage in embryonic development, during which the totipotent zygote goes through zygotic genome activation (ZGA) at 2-cell stage, and then generates the first two cell lineages, trophectodem (TE), the inner cell mass (ICM) at the blastocyst stage. The nutritional requirements of the preimplantation embryo are minimal and are largely derived from the oviductal fluid in which it floats. An in vitro culture medium with only pyruvate, lactate, and glucose as nutrients, but lacking any amino acids, fats or proteins supports normal development through the 4.5 days of preimplantation stages.Extensive studies in the past have shown that lack of these metabolites during culture result in specific developmental phenotypes. Zygote cultured in the medium lacking pyruvate is viable but fails to develop beyond the 2-cell stage. Lack of glucose in the culture medium blocks preimplantation development at the morula stage. The mechanism by which specific nutrients control different developmental processes is still unclear.In this thesis, I interrogated the roles of pyruvate and glucose during mammalian embryogenesis. We found pyruvate mediated O-glycosylation and mitochondrial enzymes nuclear localization are critical steps in mammalian ZGA at 2-cell stage (Chapter 2), while glucose metabolism distinguishes TE from ICM fate at 8- to 16-cell stages (Chapter 3).In Chapter 2, we made the novel and surprising finding that a number of enzymatically active mitochondrial enzymes associated with the TCA cycle are transiently localized to the nucleus where they directly make the metabolites that are essential for ZGA and the associated global genome organization. We also found that pyruvate, O-glycosylation, and chaperones are essential for this nuclear localization. In Chapter 3, we found that at morula stage critical pathways of glucose catabolism are the pentose pathway (PPP) and the hexosamine biosynthetic pathway (HBP) and blocking these pathways recapitulate distinct aspects of the glucose phenotype. Analysis of the roles of the PPP and the HBP further showed that these pathways have non-over lapping roles in the regulation of specific transcription factors that are essential for the establishment of the TE fate
Blood Scent
No full textBlood cell production is tightly regulated by cell-intrinsic mechanisms and environmental factors. The study by Utpal Banerjee and colleagues and colleagues reveals that, in Drosophila, olfactory signals control hematopoietic progenitor maintenance, thus uncovering a physiological link between sensory perception and hematopoietic response to environmental stress
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Sequential activation of NFkB, JNK, and cytokine signaling in the Drosophila blood system in response to distal injury
No full textIn mammals, injury-induced inflammation is mediated by Toll-like receptor (TLR)/NF-κB signaling in blood cells. Although Toll signaling is conserved in Drosophila, how the blood system senses and responds to injury remains largely unknown. By contrast, Toll pathway activation in the context of humoral immunity has been well characterized in Drosophila, focusing primarily on the adult fat body. In this study, we show that epidermal injury in Drosophila larvae causes rapid activation of Toll signaling in blood cells, and is largely independent of the pathway that is known to activate Toll in response to infection. We also show that Jun kinase signaling is activated by injury rapidly under control of Toll signaling, but only Toll contribute to the delayed downstream activation of cytokine-like signaling. It has been previously shown that epidermal injury causes blood cell differentiation in Drosophila; however the underlying molecular mechanism was unknown. Our work demonstrates that Toll and cytokine-like (JAK/STAT) signaling are required sequentially for injury-induced blood cell differentiation. Future studies aiming at understanding how epidermal injury initiates signals that leads to Toll activation may be of specific relevance to similar scenarios in mammalian injury responses
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A Performance Analysis of the Berkeley UPC Compiler
No full textUnified Parallel C (UPC) is a parallel language that uses a Single Program Multiple Data (SPMD) model of parallelism within a global address space. The global address space is used to simplify programming, especially on applications with irregular data structures that lead to fine-grained sharing between threads. Recent results have shown that the performance of UPC using a commercial compiler is comparable to that of MPI [7]. In this paper we describe a portable open source compiler for UPC. Our goal is to achieve a similar performance while enabling easy porting of the compiler and runtime, and also provide a framework that allows for extensive optimizations. We identify some of the challenges in compiling UPC and use a combination of micro-benchmarks and application kernels to show that our compiler has low overhead for basic operations on shared data and is competitive, and sometimes faster than, the commercial HP compiler. We also investigate several communication optimizations, and show significant benefits by hand-optimizing the generated code
FIG. 5 in A New Genus and Two New Species of Arboreal Toads from the Highlands of Sumatra with a Phylogeny of Sundaland Toad Genera
No full textFIG. 5.—Habitat of Sigalegalephrŋnus mandailinguensis—a view of the rainforest at the edge of an inactive solphatara field on the northeastern slope of Gunung Sorikmarapi where the holotype was found (upper); and first author at the entrance of the subterranean hollow where the holotype was collected (lower).Published as part of Smart, Utpal, Sarker, Goutam C., Arifin, Umilaela, Harvey, Michael B., Sidik, Irvan, Hamidy, Amir, Kurniawan, Nia & Smith, Eric N., 2017, Herpetologica 73 (1) on pages 63-75, DOI: 10.1655/Herpetologica-D-16-00041, http://zenodo.org/record/771643
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No full textBlood progenitors within the lymph gland, a larval organ that supports hematopoiesis in Drosophila melanogaster, are maintained by integrating signals emanating from niche-like cells and those from differentiating blood cells. We term the signal from differentiating cells the ‘equilibrium signal’ in order to distinguish it from the ‘niche signal’. Earlier we showed that equilibrium signaling utilizes Pvr (the Drosophila PDGF/VEGF receptor), STAT92E, and adenosine deaminase-related growth factor A (ADGF-A) (Mondal et al., 2011). Little is known about how this signal initiates during hematopoietic development. To identify new genes involved in lymph gland blood progenitor maintenance, particularly those involved in equilibrium signaling, we performed a genetic screen that identified bip1 (bric à brac interacting protein 1) and Nucleoporin 98 (Nup98) as additional regulators of the equilibrium signal. We show that the products of these genes along with the Bip1-interacting protein RpS8 (Ribosomal protein S8) are required for the proper expression of Pvr
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