SRI International

About: SRI International is a nonprofit organization based out in Menlo Park, California, United States. It is known for research contribution in the topics: Ionosphere & Laser. The organization has 7222 authors who have published 13102 publications receiving 660724 citations. The organization is also known as: Stanford Research Institute & SRI.

Semantic-head-driven generation

Abstract: We present an algorithm for generating strings from logical form encodings that improves upon previous algorithms in that it places fewer restrictions on the class of grammars to which it is applicable. In particular, unlike a previous bottom-up generator, it allows use of semantically nonmonotonic grammars, yet unlike top-down methods, it also permits left-recursion. The enabling design feature of the algorithm is its implicit traversal of the analysis tree for the string being generated in a semantic-head-driven fashion.

Activation of metallothionein gene expression by hypoxia involves metal response elements and metal transcription factor-1.

Abstract: Metallothioneins (MTs) are a family of stress-induced proteins with diverse physiological functions, including protection against metal toxicity and oxidants. They may also contribute to the regulation of cellular proliferation, apoptosis, and malignant progression. We reported previously that the human (h)MT-IIA isoform is induced in carcinoma cells (A431, SiHa, and HT29) exposed to low oxygen, conditions commonly found in solid tumors. The present study demonstrates that the genes for hMT-IIA and mouse (m)MT-I are transcriptionally activated by hypoxia through metal response elements (MREs) in their proximal promoter regions. These elements bind metal transcription factor-1 (MTF-1). Deletion and mutational analyses of the hMT-IIA promoter indicated that the hMRE-a element is essential for basal promoter activity and for induction by hypoxia, but that other elements contribute to the full transcriptional response. Functional studies of the mMT-I promoter demonstrated that at least two other MREs (mMRE-d and mMRE-c) are responsive to hypoxia. Multiple copies of either hMRE-a or mMRE-d conferred hypoxia responsiveness to a minimal MT promoter. Mouse MT-I gene transcripts in fibroblasts with targeted deletions of both MTF-1 alleles (MTF-1(-/-); dko7 cells) were not induced by zinc and showed low responsiveness to hypoxia. A transiently transfected MT promoter was unresponsive to hypoxia or zinc in dko7 cells, but inductions were restored by cotransfecting a mouse MTF-1 expression vector. Electrophoretic mobility shift assays detected a specific protein-DNA complex containing MTF-1 in nuclear extracts from hypoxic cells. Together, these results demonstrate that hypoxia activates MT gene expression through MREs and that this activation involves MTF-1.

The Pathway Tools cellular overview diagram and Omics Viewer

Abstract: The Pathway Tools cellular overview diagram is a visual representation of the biochemical network of an organism. The overview is automatically created from a Pathway/Genome Database describing that organism. The cellular overview includes metabolic, transport and signaling pathways, and other membrane and periplasmic proteins. Pathway Tools supports interrogation and exploration of cellular biochemical networks through the overview diagram. Furthermore, a software component called the Omics Viewer provides visual analysis of whole-organism datasets using the overview diagram as an organizing framework. For example, gene expression and metabolomics measurements, alone or in combination, can be painted onto the overview, as can computed whole-organism datasets, such as predicted reaction-flux values. The cellular overview and Omics Viewer provide a mechanism whereby biologists can apply the pattern-recognition capabilities of the human visual system to analyze large-scale datasets in a biologically meaningful context. SRI's BioCyc.org website provides overview diagrams for more than 200 organisms. This article describes enhancements to the overview made since a 1999 publication, including the automatic layout capability, expansion of the cellular machinery that it includes, new semantic zooming and poster-generating capabilities, and extension of the Omics Viewer to support painting of metabolites, animations and zooming to individual pathway diagrams.

Order-Sorted Equational Computation

Abstract: Publisher Summary This chapter discusses order-sorted equational computation. Many-sorted equational logic is the basis for algebraic specifications, rewriting techniques, unification theory, and equational programming. In the standard approach, sorts are unrelated and can be thought of as denoting disjoint sets. Order-sorted equational logic improves the expressivity of many-sorted equational logic by adding the notion of subsorts. The standard example of an abstract data type, stacks of natural numbers, is specified in order-sorted equational logic. It is known that defining a less or equal test for integers with unconditional equations not using subsorts is complicated; one has to introduce an auxiliary function and an auxiliary sort. These complications disappear if one uses conditional equations, but verification methods for the confluence of conditional rewriting systems are complicated and in most cases not practical. The chapter presents the verification methods for confluence extend to order-sorted unconditional rewriting systems.