Execution of the SimSET Monte Carlo PET/SPECT Simulator in the Condor Distributed Computing Environment

SimSET is a package for simulation of emission tomography data sets. Condor is a popular distributed computing environment. Simple C/C++ applications and shell scripts are presented which allow the execution of SimSET on the Condor environment. This is accomplished without any modification to SimSET by executing multiple instances and using its combinebin utility. This enables research facilities without dedicated parallel computing systems to utilize the idle cycles of desktop workstations to greatly reduce the run times of their SimSET simulations. The necessary steps to implement this approach in other environments are presented along with sample results

Software to compute infinitesimal symmetries of exterior differenial systems, with applications

A description is given of a software package to compute symmetries of partial differential equations, using computer algebra. As an application, the computation of higher-order symmetries of the classical Boussinesq equation is given leading to the recursion operator for symmetries in a straightforward way. Nonlocal symmetries for the Federbush model are obtained yielding the linearization of the model

Functional mechanism study of the allelochemical myrigalone A identifies a group of ultrapotent inhibitors of ethylene biosynthesis in plants

Allelochemicals represent a class of natural products released by plants as root, leaf, and fruit exudates that interfere with the growth and survival of neighboring plants. Understanding how allelochemicals function to regulate plant responses may provide valuable new approaches to better control plant function. One such allelochemical, Myrigalone A (MyA) produced by Myrica gale, inhibits seed germination and seedling growth through an unknown mechanism. Here, we investigate MyA using the tractable model Dictyostelium discoideum and reveal that its activity depends on the conserved homolog of the plant ethylene synthesis protein 1-aminocyclopropane-1-carboxylic acid oxidase (ACO). Furthermore, in silico modeling predicts the direct binding of MyA to ACO within the catalytic pocket. In D. discoideum, ablation of ACO mimics the MyA-dependent developmental delay, which is partially restored by exogenous ethylene, and MyA reduces ethylene production. In Arabidopsis thaliana, MyA treatment delays seed germination, and this effect is rescued by exogenous ethylene. It also mimics the effect of established ACO inhibitors on root and hypocotyl extension, blocks ethylene-dependent root hair production, and reduces ethylene production. Finally, in silico binding analyses identify a range of highly potent ethylene inhibitors that block ethylene-dependent response and reduce ethylene production in Arabidopsis. Thus, we demonstrate a molecular mechanism by which the allelochemical MyA reduces ethylene biosynthesis and identify a range of ultrapotent inhibitors of ethylene-regulated responses

Transmutations and spectral parameter power series in eigenvalue problems

We give an overview of recent developments in Sturm-Liouville theory concerning operators of transmutation (transformation) and spectral parameter power series (SPPS). The possibility to write down the dispersion (characteristic) equations corresponding to a variety of spectral problems related to Sturm-Liouville equations in an analytic form is an attractive feature of the SPPS method. It is based on a computation of certain systems of recursive integrals. Considered as families of functions these systems are complete in the $L_{2}$-space and result to be the images of the nonnegative integer powers of the independent variable under the action of a corresponding transmutation operator. This recently revealed property of the Delsarte transmutations opens the way to apply the transmutation operator even when its integral kernel is unknown and gives the possibility to obtain further interesting properties concerning the Darboux transformed Schr\"{o}dinger operators. We introduce the systems of recursive integrals and the SPPS approach, explain some of its applications to spectral problems with numerical illustrations, give the definition and basic properties of transmutation operators, introduce a parametrized family of transmutation operators, study their mapping properties and construct the transmutation operators for Darboux transformed Schr\"{o}dinger operators.Comment: 30 pages, 4 figures. arXiv admin note: text overlap with arXiv:1111.444

Estimates of free and bound indole-3-acetic acid and zeatin levels in relation to regulation of apical dominance and tiller release in oat shoots

Oat stem segments containing quiescent lateral (tiller) buds during times of strong apical dominance, and growing buds released from this inhibition, were collected for analysis of native auxin and cytokinins. Free IAA and IAA conjugates were determined by a 14 C-IAA and 14 C-IBA double isotope dilution assay. Free zeatin (Z), zeatin riboside (Z-r), and their glucoside conjugates were purified from butanol-soluble fractions by means of a cellulose phosphate exchanger and thin-layer chromatography. Hormones were analyzed by gas chromatography and mass spectrometry (GC-MS). Results of these analyses indicate that changes in free and bound IAA within the stem do not correlate well with the release of tiller buds (as brought about by decapitation, gravistimulation, or the emergence of the inflorescence). However, increases in Z-r levels are well correlated with tiller release. The glucoside conjugate of Z-r may act as a storage form of cytokinin in quiescent tiller buds. In light of these results, we find that the auxin-cytokinin ratio in oat stem segments is shifted during tillerPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45928/1/344_2005_Article_BF02042250.pd

From types to sets by local type definitions in higher-order logic

Types in Higher-Order Logic (HOL) are naturally interpreted as nonempty sets—this intuition is reflected in the type definition rule for the HOL-based systems (including Isabelle/HOL), where a new type can be defined whenever a nonempty set is exhibited. However, in HOL this definition mechanism cannot be applied inside proof contexts. We propose a more expressive type definition rule that addresses the limitation and we prove its soundness. This higher expressive power opens the opportunity for a HOL tool that relativizes type-based statements to more flexible set-based variants in a principled way. We also address particularities of Isabelle/HOL and show how to perform the relativization in the presence of type classes

Bioavailability in soils

The consumption of locally-produced vegetables by humans may be an important exposure pathway for soil contaminants in many urban settings and for agricultural land use. Hence, prediction of metal and metalloid uptake by vegetables from contaminated soils is an important part of the Human Health Risk Assessment procedure. The behaviour of metals (cadmium, chromium, cobalt, copper, mercury, molybdenum, nickel, lead and zinc) and metalloids (arsenic, boron and selenium) in contaminated soils depends to a large extent on the intrinsic charge, valence and speciation of the contaminant ion, and soil properties such as pH, redox status and contents of clay and/or organic matter. However, chemistry and behaviour of the contaminant in soil alone cannot predict soil-to-plant transfer. Root uptake, root selectivity, ion interactions, rhizosphere processes, leaf uptake from the atmosphere, and plant partitioning are important processes that ultimately govern the accumulation ofmetals and metalloids in edible vegetable tissues. Mechanistic models to accurately describe all these processes have not yet been developed, let alone validated under field conditions. Hence, to estimate risks by vegetable consumption, empirical models have been used to correlate concentrations of metals and metalloids in contaminated soils, soil physico-chemical characteristics, and concentrations of elements in vegetable tissues. These models should only be used within the bounds of their calibration, and often need to be re-calibrated or validated using local soil and environmental conditions on a regional or site-specific basis.Mike J. McLaughlin, Erik Smolders, Fien Degryse, and Rene Rietr

Radon and childhood cancer

British Journal of Cancer (2002) 87, 1336–1337. doi:10.1038/sj.bjc.6600671 www.bjcancer.co