Showing papers by "Michigan Technological University published in 1994"

Wolves, Moose, and Tree Rings on Isle Royale

Abstract: Investigation of tree growth in Isle Royale National Park in Michigan revealed the influence of herbivores and carnivores on plants in an intimately linked food chain. Plant growth rates were regulated by cycles in animal density and responded to annual changes in primary productivity only when released from herbivory by wolf predation. Isle Royale's dendrochronology complements a rich literature on food chain control in aquatic systems, which often supports a trophic cascade model. This study provides evidence of top-down control in a forested ecosystem.

Compiler optimizations for improving data locality

Abstract: In the past decade, processor speed has become significantly faster than memory speed. Small, fast cache memories are designed to overcome this discrepancy, but they are only effective when programs exhibit data locality. In this paper, we present compiler optimizations to improve data locality based on a simple yet accurate cost model. The model computes both temporal and spatial reuse of cache lines to find desirable loop organizations. The cost model drives the application of compound transformations consisting of loop permutation, loop fusion, loop distribution, and loop reversal. We demonstrate that these program transformations are useful for optimizing many programs.To validate our optimization strategy, we implemented our algorithms and ran experiments on a large collection of scientific programs and kernels. Experiments with kernels illustrate that our model and algorithm can select and achieve the best performance. For over thirty complete applications, we executed the original and transformed versions and simulated cache hit rates. We collected statistics about the inherent characteristics of these programs and our ability to improve their data locality. To our knowledge, these studies are the first of such breadth and depth. We found performance improvements were difficult to achieve because benchmark programs typically have high hit rates even for small data caches; however, our optimizations significantly improved several programs.

Measuring functional cohesion

Abstract: We examine the functional cohesion of procedures using a data slice abstraction. Our analysis identifies the data tokens that lie on more than one slice as the "glue" that binds separate components together. Cohesion is measured in terms of the relative number of glue tokens, tokens that lie on more than one data slice, and super-glue tokens, tokens that lie on all data slices in a procedure, and the adhesiveness of the tokens. The intuition and measurement scale factors are demonstrated through a set of abstract transformations. >

On global sequence alignment.

Abstract: We present a dynamic programming algorithm for computing a best global alignment of two sequences. The proposed algorithm is robust in identifying any of several global relationships between two sequences. The algorithm delivers a best alignment of two sequences in linear space and quadratic time. We also describe a multiple alignment algorithm based on the pairwise algorithm. Both algorithms have been implemented as portable C programs. Experimental results indicate that for a commonly used set of gap penalties, the new programs produce more satisfactory alignments on sequences of various lengths than some existing pairwise and multiple programs based on the dynamic programming algorithm of Needleman and Wunsch.

Modification of lignin biosynthesis in transgenic Nicotiana through expression of an antisense O-methyltransferase gene from Populus.

Abstract: An aspen lignin-specific O-methyltransferase (bi-OMT; S-adenosyl-L-methionine: caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase, EC 2.1.1.68) antisense sequence in the form of a synthetic gene containing the cauliflower mosaic virus 35S gene sequences for enhancer elements, promoter and terminator was stably integrated into the tobacco genome and inherited in transgenic plants with a normal phenotype. Leaves and stems of the transgenes expressed the antisense RNA and the endogenous tobacco bi-OMT mRNA was suppressed in the stems. Bi-OMT activity of stems was decreased by an average of 29% in the four transgenic plants analyzed. Chemical analysis of woody tissue of stems for lignin building units indicated a reduced content of syringyl units in most of the transgenic plants, which corresponds well with the reduced activity of bi-OMT. Transgenic plants with a suppressed level of syringyl units and a level of guaiacyl units similar to control plants were presumed to have lignins of distinctly different structure than control plants. We concluded that regulation of the level of bi-OMT expression by an antisense mechanism could be a useful tool for genetically engineering plants with modified lignin without altering normal growth and development.

14C Allocation in tree-soil systems.

Abstract: We studied whole-tree C allocation with special emphasis on the quantification of C allocation to roots and root respiration. To document seasonal patterns of C allocation, 2-year-old hybrid poplar trees greater than 3 m tall were labeled with (14)CO(2) in a large Plexiglas chamber in the field, in July and September. Climate and CO(2) concentration were controlled to track ambient conditions during labeling. Individual tree canopy CO(2) assimilation averaged 3.8 micromol CO(2) m(-2) s(-1) (12.9 g C day(-1) tree(-1)) in July and 6.2 micromol CO(2) m(-2) s(-1) (9.8 g C day(-1) tree(-1)) in September. Aboveground dark respiration was 12% of net daytime C fixation in July and 15% in September. Specific activity of root-soil respiration peaked 2 days after labeling and stabilized to less than 5% of maximum 2 weeks later. Low specific activity of root-soil respiration and a labeled pool of root C demonstrated that current photosynthate was the primary source of C for root growth and maintenance during the growing season. Root respiration averaged 20% of total soil respiration in both July and September based on the proportion of labeled C respired to labeled C fixed. In July, 80% of the recovered (14)C was found above ground and closely resembled the weight distribution of the growing shoot. By September, 51% of the recovered (14)C was in the root system and closely resembled the weight distribution of different size classes of roots. The finding that the distribution of biomass and (14)C were similar verified that the C introduced during labeling followed normal seasonal translocation pathways. Results are compared to smaller scale labeling studies and the suitability of the approach for studying long-term C fluxes is discussed.

Improving the ratio of memory operations to floating-point operations in loops

Abstract: Over the past decade, microprocessor design strategies have focused on increasing the computational power on a single chip. Because computations often require more data from cache per floating-point operation than a machine can deliver and because operations are pipelined, idle computational cycles are common when scientific applications are executed. To overcome these bottlenecks, programmers have learned to use a coding style that ensures a better balance between memory references and floating-point operations. In our view, this is a step in the wrong direction because it makes programs more machine-specific. A programmer should not be required to write a new program version for each new machine; instead, the task of specializing a program to a target machine should be left to the compiler.But is our view practical? Can a sophisticated optimizing compiler obviate the need for the myriad of programming tricks that have found their way into practice to improve the performance of the memory hierarchy? In this paper we attempt to answer that question. To do so, we develop and evaluate techniques that automatically restructure program loops to achieve high performance on specific target architectures. These methods attempt to balance computation and memory accesses and seek to eliminate or reduce pipeline interlock. To do this, they estimate statically the balance between memory operations and floating-point operations for each loop in a particular program and use these estimates to determine whether to apply various loop transformations.Experiments with our automatic techniques show that integer-factor speedups are possible on kernels. Additionally, the estimate of the balance between memory operations and computation, and the application of the estimate are very accurate—experiments reveal little difference between the balance achieved by our automatic system that is made possible by hand optimization.

Specificity of Hydrolysis of Phytic Acid by Alkaline Phytase from Lily Pollen

Abstract: Phytases are the primary enzymes responsible for the hydrolysis of phytic acid, myo-inositol-1,2,3,4,5,6-hexakisphosphate (I-1,2,3,4,5,6-P6). A number of phytases with varying specificities, properties, and localizations hydrolyze phytic acid present in cells. The specificity of hydrolysis of phytic acid by alkaline phytase from lily (Lilium longiflorum L.) pollen is described. Structures of the intermediate inositol phosphates and the final product were established by a variety of nuclear magnetic resonance techniques (1H-, 31P-, and 31P-1H-detected multiple quantum coherence spectroscopy, and total correlation spectroscopy). On the basis of the structures identified we have proposed a scheme of hydrolysis of phytic acid. Initial hydrolysis of the phosphate ester occurs at the D-5 position of phytic acid to yield the symmetrical I-1,2,3,4,6-P5. The two subsequent dephosphorylations occur adjacent to the D-5 hydroxyl group to yield I-1,2,3-P3 as the final product. Alkaline phytase differs from other phytases in the specificity of hydrolysis of phosphate esters on the inositol ring, its high substrate specificity for phytic acid, and biochemical properties such as susceptibility to activation by calcium and inhibition by fluoride. The physiological significance of alkaline phytase and the biological role of I-1,2,3-P3 remain to be identified.

Application of nonlinear dynamics and chaos to ferroresonance in distribution systems

Abstract: Ferroresonant overvoltages or undervoltages can occur in cable-fed power transformer installations when single phase switching or interrupting is practiced. This paper identifies the ferroresonant circuit as a nonlinear dynamical system. Analysis and classification methods are presented which provide new insight into the global behavior of ferroresonance. The concepts presented offer potential for progress in the areas of transformer model development and evaluation, analysis and prediction of ferroresonance, and distribution system design and operation. Measurements from a typical five-legged core transformer installation are used to illustrate the application of nonlinear dynamics and chaotic systems to the problem of ferroresonance. >

Modeling of mechanical alloying: Part I. deformation, coalescence, bdand fragmentation mechanisms

Abstract: A model of the mechanical alloying process, applicable to a single collision event involving ductile species, is developed. Simple physical models are constructed that allow development of analytical expressions for particle shape and hardness changes during a collision and stipulation of criteria for particle fracture and cold welding. These provide a“snapshot” of that which transpires during a single collision event. The model also accounts for the heterogeneity of deformation within the powder trapped between colliding media. This heterogeneity, together with the model criteria, can then be incorporated within a computational scheme capable of predictive description of the evolution of powder morphology and properties during mechanical alloying, as will be described in a subsequent article.

An autonomous vision-based mobile robot

Abstract: This paper describes the theoretical development and experimental implementation of a complete navigation procedure for use in an autonomous mobile robot for structured environments. Estimates of the vehicle's position and orientation are based on the rapid observation of visual cues located at discrete positions within the environment. The extended Kalman filter is used to combine these visual observations with sensed wheel rotations to produce optimal estimates continuously. The complete estimation procedure, as well as the control algorithm, developed are time independent. A naturally suitable quantity involving wheel rotations is used as the independent variable. One consequence of this choice is that the vehicle speed can be specified independently of the estimation and control algorithms. Reference paths are "taught" by manually leading the vehicle through the desired path. Estimates produced by the extended Kalman filter during this teaching session are then used to represent the geometry of the path. The tracking of taught reference paths is accomplished by controlling the position and orientation of the vehicle relative to the reference path. Time-independence path tracking has necessitated the development of a novel, geometry-based means for advancing along the reference path. >

Agrobacterium-mediated transformation of quaking aspen (Populus tremuloides) and regeneration of transgenic plants.

Abstract: Agrobacterium-mediated gene transformation of Populus tremuloides Michx was accomplished by co-cultivation of leaf disks excised from greenhouse plants with Agrobacterium tumefaciens containing a binary Ti-plasmid vector harboring chimeric neomycin phosphotransferase (NPT II) and s-glucuronidase (GUS) genes. Shoot regeneration in the presence of kanamycin was achieved when thidiazuron (TDZ) was used as a plant growth regulator. Transformation was verified by amplification of NPT II and GUS gene fragments from genomic DNA of transgenic plants with polymerase chain reaction (PCR) and integration of these genes into nuclear genome of transgenic plants was confirmed by genomic Southern hybridization analysis. Histochemical assay revealed the expression of GUS gene in leaf, stem and root tissues of transgenic plants, further confirming the integration and expression of T-DNA in these plants. This protocol allows effective transformation and regeneration of quaking aspen using greenhouse-grown materials as an explant source. Whole plant regeneration from cuttings of fieldgrown mature quaking aspen and hybrid poplar (P. alba x P. grandidentata) was also readily achieved by using this protocol, which represents a potential system for producing transgenic quaking aspen and hybrid poplar of valuable genotypes.

An algorithm for identifying regions of a DNA sequence that satisfy a content requirement.

Abstract: We present a dynamic programming algorithm for identifying regions of a DNA sequence that meet a user-specified compositional requirement. Applications of the algorithm include finding C + G-rich regions, locating TA + CG-deficient regions, identifying CpG islands, and finding regions rich in periodical three-base patterns. The algorithm has an advantage over the simple window method in that the algorithm shows the exact location of each identified region. The algorithm has been implemented as a portable C program called LCP (Local Content Program). LCP is extremely efficient in computer time and memory; it instantly locates all regions of a long DNA sequence meeting a given requirement. The LCP program was used to analyze the rabbit alpha-like globin gene cluster sequence.

Identification of a maize root transcript expressed in the primary response to nitrate: characterization of a cDNA with homology to ferredoxin-NADP+ oxidoreductase

Abstract: To more fully understand the biochemical and molecular events which occur in plants exposed to nitrate, cDNAs whose accumulation was enhanced in nitrate- and cycloheximide-treated maize (Zea mays L. W64A × W182E) roots were isolated. The 340 bp Zmrprn 1 (for Zea mays root primary response to nitrate) cDNA also hybridized with a probe enriched for nitrate-induced sequences, and was characterized further. Sequence analysis of a near full-length cDNA (Zmrprn 1A) showed strong homology (>90% amino acid identity) with a root ferredoxin-NADP+ oxidoreductase (FNR) of rice, and 45–50% amino acid identity with leaf FNR genes. When expressed in Escherichia coli, the Zmrprn 1A cDNA produced a protein with NADPH: ferricyanide reductase activity, consistent with the enzymatic properties of an FNR. The Zmrprn 1 cDNA hybridized with a 1.4 kb transcript which was expressed in the maize root primary response to nitrate. That is, mRNA levels in roots increased rapidly and transiently in response to external nitrate, and low levels of nitrate (10 μM) induced transcript accumulation. The accumulation of the Zmrprn 1 transcript was not prevented by cycloheximide, indicating that the cellular factor(s) required for expression were constitutively present in maize roots. The Zmrprn 1 mRNA accumulated specifically in response to nitrate, since neither K+ nor NH4 + treatment of roots caused transcript accumulation. Maize leaves had about 5% of the transcript level found in roots, indicating a strong preference for expression of Zmrprn 1 in roots. Analysis of maize genomic DNA indicated the presence of only a single gene or very small gene family for the Zmrprn 1. Together, the data indicate that Zmrprn 1A encodes a nitrate regulated maize root FNR.

Adaptive Quaternion Feedback Regulation for Eigenaxis Rotations

Abstract: A controller to rotate a rigid body between two successive orientations is designed Particular features are the fact that it is based on the quaternion approach, known to provide singularity-free attitude description, and it is adaptive in the sense that it does not need specific knowledge of the inertia matrix Global stability of the overall controller is proved analytically and tested in computer simulations In this paper, we design a nonlinear adaptive controller that per- forms vehicle orientation in the presence of large uncertainties of the inertia matrix The concept of adaptive control for linear time- invariant systems dates back to the 1950s although reliable designs of proven stability did not appear before the late 1970s14'15 Both di- rect and indirect adaptive control schemes are presented The direct adaptive controller has the advantage of simplicity in the imple- mentation, since it is based on a simple gradient-type adaptation law However, the indirect approach we present, although of more complex implementation, is based on a recursive least-squares iden- tification algorithm that has the advantage of converging faster In general, adaptive controllers of nonlinear systems are based on a linearized model of the plant, and stability can be shown only locally In a few cases the particular structure of a nonlinear system lends itself to a globally stable adaptive control algorithm, such as the case of robotic manipulators16 The adaptive controller presented below falls in this category, for which we can show global stability of the overall system composed of the plant and the controller with recursive estimates of the inertia matrix Eigenaxis rotation is presented in Sec II Three control tech- niques are given next: a sliding-mode technique in Sec Ill, direct adaptive control in Sec IV followed by an indirect approach in Sec V, whereas examples and conclusions are given in Sec VI and VII, respectively

Paleolimnological study of copper mining around Lake Superior: Artificial varves from Portage Lake provide a high resolution record

Abstract: On the Keweenaw Peninsula region of Lake Superior, -0.5 Gt of copper mine tailings were dumped along rivers, lakes, and connecting waterways between 1850 and 1968 -an era of active copper and silver mining. In the low-energy environment of Portage Lake, a part of the Keweenaw Waterway, clay particles from stamp sand discharges created artificially varved lake sediments that preserved a remarkably detailed record. Measurements of these varves, in conjunction with radiodating techniques, allow precise detcrminations of deposition rates, sediment, and Cu fluxes. Concentration and flux profiles produce fundamentally different patterns. Copper concentrations have remained high in sediments despite complete cessation of active tailings discharge. However, densitometer scans of X-rayed cores and flux calculations at sites closest to sluicing locations reveal a good correspondence with the historic record of stamp sand production. Sedimentation rates and Cu fluxes have declined steadily since cessation of native copper mining, although elevated Cu levels continue to circulate in the ecosystem. Comparisons of Cu profiles from sediment cores across eastern Lake Superior suggest widespread signatures of mining and major contribution to sediments.

A.numerical simulation of gas flow during coal/gas outbursts

Abstract: A model of the gas flow in airways during an instantaneous outburst of coal and gas is formulated and solved numerically using MacCormack's explicit finite-difference scheme. This model is based on the assumption that geological structures, in-situ stresses and high-gas-pressure gradients play important roles in initiating an outburst, with the gas content and gas-pressure gradients being the most dominant factors. The fluid-dynamic processes that occur after an outburst are computed by the numerical integration of the complete time-dependent Navier-Stokes equations. The mixture velocity, the density and the gas-concentration profiles in both time and space domains (immediately after an outburst) are presented. The global results are useful in gaining an improved understanding of gas-flow patterns during coal/gas outbursts and in determining the range of the disturbance so that effective methods of control can be developed.

A monte carlo method for simulating associating fluids

Abstract: We present association biased Monte Carlo (ABMC), a Monte Carlo method, which is ergodic, microscopically reversible, and specifically designed to simulate associating fluids with long‐ranged center‐to‐center interactions. The canonical ensemble (NVT) algorithm biases sampling to regions of configuration space where particle association is likely to occur, and provides efficient simulation of associating fluids over a broad range of densities. The usual canonical ensemble (NVT) thermodynamic variables (ensemble average internal energy and pressure), as well as the pair distribution functions are presented. The distributions of associated clusters are presented at a selection of state points and are compared with predictions of thermodynamic perturbation theory for the model system. We also present the simulation results for a symmetric, binary associating fluid with a single site on each particle.

Environmental embrittlement of single crystal and thermomechanically processed B2-ordered iron aluminides

Abstract: Environmental embrittlement contributes to the poor ductility of iron aluminides. Elongations in dry environments, such as vacuum or dry oxygen, are considerably greater than in air. Moisture in air is the source of the embrittlement and it is believed that the water vapor reacts with aluminum atoms at the crack tip to produce hydrogen, which then causes embrittlement. In order to expand the use of iron aluminides commercially, this poor room temperature ductility has to be overcome. This has been accomplished in part by alloying with chromium and by thermomechanical processing (T/M-P) schemes. In fact, significant increases in ductility in air have been reported for an alloy containing 5% Cr which had been warm rolled to produce a partially recrystallized microstructure. The effects of chromium are not well understood as of yet, but it has been postulated that the T/M-P effect is caused by the presence of the partially recrystallized microstructure, which reduces the environmental susceptibility by decreasing the number of transverse grain boundaries, thus reducing hydrogen penetration into the material. This argument assumes that grain boundaries have a large effect on embrittlement by controlling hydrogen ingress into the material. The objectives of this work are to determine the rolesmore » grain boundaries have in the environmental embrittlement of iron aluminides and in the T/M-P effect observed in these materials. Alloys of several compositions were thermomechanically processed, heat treated and then tensile tested in environments of dry oxygen and moist air. Single crystals containing 35% Al were also tested in oxygen and air.« less