LIME : Software for 3-D visualization, interpretation, and communication of virtual geoscience models

Parts of LIME have been developed to address research requirements in projects funded by the Research Council of Norway (RCN) through the Petromaks and Petromaks 2 programs. The following grants are acknowledged: 153264 (VOG [Virtual Outcrop Geology]; with Statoil ASA), 163316 (Carbonate Reservoir Geomodels [IRIS (International Research Institute of Stavanger)]), 176132 (Paleokarst Reservoirs [Uni Research CIPR]), 193059 (EUSA; with FORCE Sedimentology and Stratigraphy Group), 234152 (Trias North [University of Oslo]; with Deutsche Erdoel AG, Edison, Lundin, Statoil, and Tullow), 234111 (VOM2MPS [Uni Research CIPR]; with FORCE Sedimentology and Stratigraphy Group), as well as SkatteFUNN (RCN) project 266740. In addition, the SAFARI project consortium (http://safaridb.com) is thanked for its continued support. The OSG and wxWidgets communities are acknowledged for ongoing commitment to providing mature and powerful software libraries. All authors thank colleagues past and present for studies culminating in the presented figures: Kristine Smaadal and Aleksandra Sima (Figs. 1 and 4); Colm Pierce (Fig. 2A); Eivind Bastesen, Roy Gabrielsen and Haakon Fossen (Fig. 3); Christian Haug Eide (Fig. 7); Ivar Grunnaleite and Gunnar Sælen (Fig. 8); and Magda Chmielewska (Fig. 9). Isabelle Lecomte contributed to discussions on geospatial-geophysical data fusion. Bowei Tong and Joris Vanbiervliet are acknowledged for internal discussions during article revision. The lead author thanks Uni Research for providing a base funding grant to refine some of the presented features. Finally, authors Buckley and Dewez are grateful to Institut Carnot BRGM for the RADIOGEOM mobility grant supporting the writing of this paper. Corbin Kling and one anonymous reviewer helped improve the final manuscript.Peer reviewedPublisher PD

Linear inequalities among graph invariants: Using GraPHedron to uncover optimal relationships

Optimality of a linear inequality in finitely many graph invariants is defined through a geometric approach. For a fixed number of graph vertices, consider all the tuples of values taken by the invariants on a selected class of graphs. Then form the polytope which is the convex hull of all these tuples. By definition, the optimal linear inequalities correspond to the facets of this polytope. They are finite in number, are logically independent, and generate precisely all the linear inequalities valid on the class of graphs. The computer system GraPHedron, developed by some of the authors, is able to produce experimental data about such inequalities for a "small" number of vertices. It greatly helps in conjecturing optimal linear inequalities, which are then hopefully proved for any number of vertices. Two examples are investigated here for the class of connected graphs. First, all the optimal linear inequalities for the stability number and the number of edges are obtained. To this aim, a problem of Ore (1962) related to the Turán Theorem (1941) is solved. Second, several optimal inequalities are established for three invariants: the maximum degree, the irregularity, and the diameter. © 2008 Wiley Periodicals, Inc

Protection of the Ovine Fetal Gut against Ureaplasma-Induced Chorioamnionitis: A Potential Role for Plant Sterols

Chorioamnionitis, clinically most frequently associated with Ureaplasma, is linked to intestinal inflammation and subsequent gut injury. No treatment is available to prevent chorioamnionitis-driven adverse intestinal outcomes. Evidence is increasing that plant sterols possess immune-modulatory properties. Therefore, we investigated the potential therapeutic effects of plant sterols in lambs intra-amniotically (IA) exposed to Ureaplasma. Fetal lambs were IA exposed to Ureaplasma parvum (U. parvum, UP) for six days from 127 d–133 d of gestational age (GA). The plant sterols β-sitosterol and campesterol, dissolved with β-cyclodextrin (carrier), were given IA every two days from 122 d–131 d GA. Fetal circulatory cytokine levels, gut inflammation, intestinal injury, enterocyte maturation, and mucosal phospholipid and bile acid profiles were measured at 133 d GA (term 150 d). IA plant sterol administration blocked a fetal inflammatory response syndrome. Plant sterols reduced intestinal accumulation of proinflammatory phospholipids and tended to prevent mucosal myeloperoxidase-positive (MPO) cell influx, indicating an inhibition of gut inflammation. IA administration of plant sterols and carrier diminished intestinal mucosal damage, stimulated maturation of the immature epithelium, and partially prevented U. parvum-driven reduction of mucosal bile acids. In conclusion, we show that β-sitosterol and campesterol administration protected the fetus against adverse gut outcomes following UP-driven chorioamnionitis by preventing intestinal and systemic inflammation

Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation

Chlamydomonas reinhardtii, a unicellular green alga, has been exploited as a reference organism for identifying proteins and activities associated with the photosynthetic apparatus and the functioning of chloroplasts. Recently, the full genome sequence of Chlamydomonas was generated and a set of gene models, representing all genes on the genome, was developed. Using these gene models, and gene models developed for the genomes of other organisms, a phylogenomic, comparative analysis was performed to identify proteins encoded on the Chlamydomonas genome which were likely involved in chloroplast functions (or specifically associated with the green algal lineage); this set of proteins has been designated the GreenCut. Further analyses of those GreenCut proteins with uncharacterized functions and the generation of mutant strains aberrant for these proteins are beginning to unmask new layers of functionality/regulation that are integrated into the workings of the photosynthetic apparatus

Defects in tRNA Modification Associated with Neurological and Developmental Dysfunctions in Caenorhabditis elegans Elongator Mutants

Elongator is a six subunit protein complex, conserved from yeast to humans. Mutations in the human Elongator homologue, hELP1, are associated with the neurological disease familial dysautonomia. However, how Elongator functions in metazoans, and how the human mutations affect neural functions is incompletely understood. Here we show that in Caenorhabditis elegans, ELPC-1 and ELPC-3, components of the Elongator complex, are required for the formation of the 5-carbamoylmethyl and 5-methylcarboxymethyl side chains of wobble uridines in tRNA. The lack of these modifications leads to defects in translation in C. elegans. ELPC-1::GFP and ELPC-3::GFP reporters are strongly expressed in a subset of chemosensory neurons required for salt chemotaxis learning. elpc-1 or elpc-3 gene inactivation causes a defect in this process, associated with a posttranscriptional reduction of neuropeptide and a decreased accumulation of acetylcholine in the synaptic cleft. elpc-1 and elpc-3 mutations are synthetic lethal together with those in tuc-1, which is required for thiolation of tRNAs having the 5′methylcarboxymethyl side chain. elpc-1; tuc-1 and elpc-3; tuc-1 double mutants display developmental defects. Our results suggest that, by its effect on tRNA modification, Elongator promotes both neural function and development