A layout algorithm for signaling pathways

Cataloged from PDF version of article.Visualization is crucial to the effective analysis of biological pathways. A poorly laid out pathway confuses the user, while a well laid out one improves the user's comprehension of the underlying biological phenomenon. We present a new, elegant algorithm for layout of biological signaling pathways. Our algorithm uses a force-directed layout scheme, taking into account directional and rectangular regional constraints enforced by different molecular interaction types and subcellular locations in a cell. The algorithm has been successfully implemented as part of a pathway visualization and analysis toolkit named PATIKA, and results with respect to computational complexity and quality of the layout have been found satisfactory. The algorithm may be easily adapted to be used in other applications with similar conventions and constraints as well. PATIKA version 1.0 beta is available upon request at http://www.patika.org. (C) 2004 Elsevier Inc. All rights reserved

Apparent stress-strain relationships in experimental equipment where magnetorheological fluids operate under compression mode

Abstract: This paper presents an experimental investigation of two different magnetorheological ( MR) fluids, namely, water-based and hydrocarbon-based MR fluids in compression mode under various applied currents. Finite element method magnetics was used to predict the magnetic field distribution inside the MR fluids generated by a coil. A test rig was constructed where the MR fluid was sandwiched between two flat surfaces. During the compression, the upper surface was moved towards the lower surface in a vertical direction. Stress-strain relationships were obtained for arrangements of equipment where each type of fluid was involved, using compression test equipment. The apparent compressive stress was found to be increased with the increase in magnetic field strength. In addition, the apparent compressive stress of the water-based MR fluid showed a response to the compressive strain of greater magnitude. However, during the compression process, the hydrocarbon-based MR fluid appeared to show a unique behaviour where an abrupt pressure drop was discovered in a region where the apparent compressive stress would be expected to increase steadily. The conclusion is drawn that the apparent compressive stress of MR fluids is influenced strongly by the nature of the carrier fluid and by the magnitude of the applied current

Foot Reaction Forces during Long Duration Space Flight

Musculoskeletal changes, particularly in the lower extremities, are an established consequence of long-duration space flight despite exercise countermeasures. It is widely believed that disuse and reduction in load bearing are key to these physiological changes, but no quantitative data characterizing the on-orbit movement environments currently exist. Here we present data from the Foot Experiment (E318) regarding astronaut activity on the ground and on-orbit during typical days from 4 International Space Station (ISS) crew members who flew during increments 6, 8, 11, and 12

Adolescent brain maturation and cortical folding: evidence for reductions in gyrification

Evidence from anatomical and functional imaging studies have highlighted major modifications of cortical circuits during adolescence. These include reductions of gray matter (GM), increases in the myelination of cortico-cortical connections and changes in the architecture of large-scale cortical networks. It is currently unclear, however, how the ongoing developmental processes impact upon the folding of the cerebral cortex and how changes in gyrification relate to maturation of GM/WM-volume, thickness and surface area. In the current study, we acquired high-resolution (3 Tesla) magnetic resonance imaging (MRI) data from 79 healthy subjects (34 males and 45 females) between the ages of 12 and 23 years and performed whole brain analysis of cortical folding patterns with the gyrification index (GI). In addition to GI-values, we obtained estimates of cortical thickness, surface area, GM and white matter (WM) volume which permitted correlations with changes in gyrification. Our data show pronounced and widespread reductions in GI-values during adolescence in several cortical regions which include precentral, temporal and frontal areas. Decreases in gyrification overlap only partially with changes in the thickness, volume and surface of GM and were characterized overall by a linear developmental trajectory. Our data suggest that the observed reductions in GI-values represent an additional, important modification of the cerebral cortex during late brain maturation which may be related to cognitive development

Quantitative trait loci conferring grain mineral nutrient concentrations in durum wheat 3 wild emmer wheat RIL population

Mineral nutrient malnutrition, and particularly deficiency in zinc and iron, afflicts over 3 billion people worldwide. Wild emmer wheat, Triticum turgidum ssp. dicoccoides, genepool harbors a rich allelic repertoire for mineral nutrients in the grain. The genetic and physiological basis of grain protein, micronutrients (zinc, iron, copper and manganese) and macronutrients (calcium, magnesium, potassium, phosphorus and sulfur) concentration was studied in tetraploid wheat population of 152 recombinant inbred lines (RILs), derived from a cross between durum wheat (cv. Langdon) and wild emmer (accession G18-16). Wide genetic variation was found among the RILs for all grain minerals, with considerable transgressive effect. A total of 82 QTLs were mapped for 10 minerals with LOD score range of 3.2–16.7. Most QTLs were in favor of the wild allele (50 QTLs). Fourteen pairs of QTLs for the same trait were mapped to seemingly homoeologous positions, reflecting synteny between the A and B genomes. Significant positive correlation was found between grain protein concentration (GPC), Zn, Fe and Cu, which was supported by significant overlap between the respective QTLs, suggesting common physiological and/or genetic factors controlling the concentrations of these mineral nutrients. Few genomic regions (chromosomes 2A, 5A, 6B and 7A) were found to harbor clusters of QTLs for GPC and other nutrients. These identified QTLs may facilitate the use of wild alleles for improving grain nutritional quality of elite wheat cultivars, especially in terms of protein, Zn and Fe

Supply Chain Management of Renal Transplantation

Chronic renal diseases cause substantial problems to dialysis patients and their caregivers within medical, social and economical areas. In severe cases, renal transplantation is only hope for the life of these patients. This study examines renal transplantation from supply chain management point of view. In literature, the issue of renal transplantation is usually discussed from medical point of view. However, there are scarce studies that reevaluates the transplantation procedures from supply chain perspective. The procurement, allocation and transportation of organs are called as logistics of organ transplantation. This paper examines renal transplantation in Turkey and evaluates renal allocation in particular