Showing papers by "Michigan Technological University published in 2006"

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

Abstract: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

Landau-level splitting in graphene in high magnetic fields.

Abstract: The quantum Hall (QH) effect in two-dimensional electrons and holes in high quality graphene samples is studied in strong magnetic fields up to 45 T. QH plateaus at filling factors nu = 0, +/-1, +/-4 are discovered at magnetic fields B > 20 T, indicating the lifting of the fourfold degeneracy of the previously observed QH states at nu = +/-4(absolute value(n) + 1/2), where n is the Landau-level index. In particular, the presence of the nu = 0, +/-1 QH plateaus indicates that the Landau level at the charge neutral Dirac point splits into four sublevels, lifting sublattice and spin degeneracy. The QH effect at nu = +/-4 is investigated in a tilted magnetic field and can be attributed to lifting of the spin degeneracy of the n = 1 Landau level.

A Wavelet Approach to Wideband Spectrum Sensing for Cognitive Radios

Abstract: In cognitive radio networks, the first cognitive task preceding any form of dynamic spectrum management is the sensing and identification of spectrum holes in wireless environments This paper develops a wavelet approach to efficient spectrum sensing of wideband channels The signal spectrum over a wide frequency band is decomposed into elementary building blocks of subbands that are well characterized by local irregularities in frequency As a powerful mathematical tool for analyzing singularities and edges, the wavelet transform is employed to detect and estimate the local spectral irregular structure, which carries important information on the frequency locations and power spectral densities of the subbands Along this line, a couple of wideband spectrum sensing techniques are developed based on the local maxima of the wavelet transform modulus and the multi-scale wavelet products The proposed sensing techniques provide an effective radio sensing architecture to identify and locate spectrum holes in the signal spectrum

First-principles study of the structural, electronic, and optical properties of Ga 2 O 3 in its monoclinic and hexagonal phases

Abstract: We report the results of a comprehensive study on the structural, electronic, and optical properties of Ga2O3 in its ambient, monoclinic and high-pressure, hexagonal phases in the framework of all-electron density functional theory. In both phases, the conduction band minimum is at the zone center while the valance band maximum is rather flat in the k space. The calculated electron effective mass me /m0 comes out to be 0.342 and 0.276 for -Ga2O3 and -Ga2O3, respectively. The dynamic dielectric function, reflectance, and energy-loss function for both phases are reported for a wide energy range of 0 – 50 eV. The subtle differences in electronic and optical properties can be attributed to the higher symmetry, coordination number of Ga atoms, and packing density in -Ga2O3 relative to that in -Ga2O3.

Forest carbon management in the United States: 1600-2100

Abstract: This paper reviews the effects of past forest management on carbon stocks in the United States, and the challenges for managing forest carbon resources in the 21st century. Forests in the United States were in approximate carbon balance with the atmosphere from 1600-1800. Utilization and land clearing caused a large pulse of forest carbon emissions during the 19th century, followed by regrowth and net forest carbon sequestration in the 20th century. Recent data and knowledge of the general behavior of forests after disturbance suggest that the rate of forest carbon sequestration is declining. A goal of an additional 100 to 200 Tg C/yr of forest carbon sequestration is achievable, but would require investment in inventory and monitoring, development of technology and practices, and assistance for land managers.

Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus.

Abstract: Salicin-based phenolic glycosides, hydroxycinnamate derivatives and flavonoid-derived condensed tannins comprise up to one-third of Populus leaf dry mass. Genes regulating the abundance and chemical diversity of these substances have not been comprehensively analysed in tree species exhibiting this metabolically demanding level of phenolic metabolism. Here, shikimate-phenylpropanoid pathway genes thought to give rise to these phenolic products were annotated from the Populus genome, their expression assessed by semiquantitative or quantitative reverse transcription polymerase chain reaction (PCR), and metabolic evidence for function presented. Unlike Arabidopsis, Populus leaves accumulate an array of hydroxycinnamoyl-quinate esters, which is consistent with broadened function of the expanded hydroxycinnamoyl-CoA transferase gene family. Greater flavonoid pathway diversity is also represented, and flavonoid gene families are larger. Consistent with expanded pathway function, most of these genes were upregulated during wound-stimulated condensed tannin synthesis in leaves. The suite of Populus genes regulating phenylpropanoid product accumulation should have important application in managing phenolic carbon pools in relation to climate change and global carbon cycling.

International Consortium for Atmospheric Research on Transport and Transformation (ICARTT): North America to Europe—Overview of the 2004 summer field study

Abstract: In the summer of 2004 several separate field programs intensively studied the photochemical, heterogeneous chemical and radiative environment of the troposphere over North America, the North Atlantic Ocean, and western Europe. Previous studies have indicated that the transport of continental emissions, particularly from North America, influences the concentrations of trace species in the troposphere over the North Atlantic and Europe. An international team of scientists, representing over 100 laboratories, collaborated under the International Consortium for Atmospheric Research on Transport and Transformation (ICARTT) umbrella to coordinate the separate field programs in order to maximize the resulting advances in our understanding of regional air quality, the transport, chemical transformation and removal of aerosols, ozone, and their precursors during intercontinental transport, and the radiation balance of the troposphere. Participants utilized nine aircraft, one research vessel, several ground-based sites in North America and the Azores, a network of aerosol-ozone lidars in Europe, satellites, balloon borne sondes, and routine commercial aircraft measurements. In this special section, the results from a major fraction of those platforms are presented. This overview is aimed at providing operational and logistical information for those platforms, summarizing the principal findings and conclusions that have been drawn from the results, and directing readers to specific papers for further details.

Significant enhancements of nitrogen oxides, black carbon, and ozone in the North Atlantic lower free troposphere resulting from North American boreal wildfires

Abstract: enhancements of CO, BC, NOy and NOx, with levels up to 250 ppbv, 665 ng m 3 , 1100 pptv and 135 pptv, respectively. Enhancement ratios relative to CO were variable in the plumes sampled, most likely because of variations in wildfire emissions and removalprocessesduringtransport.AnalysesofDBC/DCO,DNOy/DCOandDNOx/DCO ratios indicate that NOy and BC were on average efficiently exported in these plumes and suggest that decomposition of PAN to NOx was a significant source of NOx. High levels of NOx suggest continuing formation of O3 in these well-aged plumes. O3 levels were also significantly enhanced in the plumes, reaching up to 75 ppbv. Analysis of DO3/DCO ratios showed distinct behaviors of O3 in the plumes, which varied from significant to lower O3 production. We identify several potential reasons for the complex effects of boreal wildfire emissions on O3 and conclude that this behavior needs to be explored further in the future. These observations demonstrate that boreal wildfire emissions significantly contributed to the NOx and O3 budgets in the central North Atlantic lower free troposphere during summer 2004 and imply large-scale impacts on direct radiative forcing of the atmosphere and on tropospheric NOx and O3.

Increased N availability in grassland soils modifies their microbial communities and decreases the abundance of arbuscular mycorrhizal fungi

Abstract: Two complementary studies were performed to examine (1) the effect of 18 years of nitrogen (N) fertilization, and (2) the effects of N fertilization during one growing season on soil microbial community composition and soil resource availability in a grassland ecosystem. N was added at three different rates: 0, 5.44, and 27.2 g N m−2 y−1. In both studies, Schizachyrium scoparium was the dominant plant species before N treatments were applied. Soil microbial communities from each experiment were characterized using fatty acid methyl ester (FAME) analysis. Discriminant analysis of the FAMEs separated the three N fertilizer treatments in both experiments, indicating shifts in the composition of the microbial communities. In general, plots that received N fertilizer at low or high application rates for 18 years showed increased proportions of bacterial FAMEs and decreased fungal FAMEs. In particular, control plots contained a significantly higher proportion of fungal FAMEs C18:1(cis9) and C18:2(cis9,12) and of the arbuscular mycorrhizal fungal (AMF) FAME, C16:1(cis11), than both of the N addition treatment plots. A significant negative effect of N fertilization on the AMF FAME, C16:1(cis11), was measured in the short-term experiment. Our results indicate that high rates of anthropogenic N deposition can lead to significant changes in the composition of soil microbial communities over short periods and can even disrupt the relationship between AMF and plants.

Examining the role of cutting fluids in machining and efforts to address associated environmental/health concerns

Abstract: Cutting fluids have seen extensive use and have commonly been viewed as a required addition to high productivity and high quality machining operations. Cutting fluid related costs and health concerns associated with exposure to cutting fluid mist and a growing desire to achieve environmental sustainability in manufacturing have caused industry and academia to re-examine the role of these fluids and quantify their benefits. This work summarizes the traditional purposes of cutting fluids and reports on recent analytical and experimental research to critically examine these functions. To minimize or even eliminate the concerns associated with cutting fluid usage, several recent and novel approaches have been proposed and are examined.

Improved Concept and Model of Eddy Current Damper

Abstract: When a conductive material experiences a time-varying magnetic field, eddy currents are generated in the conductor These eddy currents circulate such that they generate a magnetic field of their own, however the field generated is of opposite polarity, causing a repulsive force The time-varying magnetic field needed to produce such currents can be induced either by movement of the conductor in the field or by changing the strength or position of the source of the magnetic field In the case of a dynamic system the conductor is moving relative to the magnetic source, thus generating eddy currents that will dissipate into heat due to the resistivity of the conductor This process of the generation and dissipation of eddy current causes the system to function as a viscous damper In a previous study, the concept and theoretical model was developed for one eddy current damping system that was shown to be effective in the suppression of transverse beam vibrations The mathematical model developed to predict the amount of damping induced on the structure was shown to be accurate when the magnet was far from the beam but was less accurate for the case that the gap between the magnet and beam was small In the present study, an improved theoretical model of the previously developed system will be formulated using the image method, thus allowing the eddy current density to be more accurately computed In addition to the development of an improved model, an improved concept of the eddy current damper configuration is developed, modeled, and tested The new damper configuration adds significantly more damping to the structure than the previously implemented design and has the capability to critically damp the beam 's first bending mode The eddy current damper is a noncontacting system, thus allowing it to be easily applied and able to add significant damping to the structure without changing dynamic response Furthermore, the previous model and the improved model will lie applied to the new damper design and the enhanced accuracy of this new theoretical model will he proven

3D finite element model of meniscectomy: changes in joint contact behavior.

Abstract: The goal of this study is to quantify changes in knee joint contact behavior following varying degrees of the medial partial meniscectomy A previously validated 3D finite element model was used to simulate 11 different meniscectomies The accompanying changes in the contact pressure on the superior surface of the menisci and tibial plateau were quantified as was the axial strain in the menisci and articular cartilage The percentage of medial meniscus removed was linearly correlated with maximum contact pressure, mean contact pressure, and contact area The lateral hemi-joint was minimally affected by the simulated medial meniscectomies The location of maximum strain and location of maximum contact pressure did not change with varying degrees of partial medial meniscectomy When 60% of the medial meniscus was removed, contact pressures increased 65% on the remaining medial meniscus and 55% on the medial tibial plateau These data will be helpful for assessing potential complications with the surgical treatment of meniscal tears Additionally, these data provide insight into the role of mechanical loading in the etiology of post-meniscectomy osteoarthritis

Predator disease out-break modulates top-down, bottom-up and climatic effects on herbivore population dynamics

Abstract: Human-introduced disease and climatic change are increasingly perturbing natural ecosystems worldwide, but scientists know very little about how they interact to affect ecological dynamics. An outbreak of canine parvovirus (CPV) in the wolf population on Isle Royale allowed us to test the transient effects of an introduced pathogen and global climatic variation on the dynamics of a three-level food chain. Following the

Extracellular matrix assembly in diatoms (bacillariophyceae). v. environmental effects on polysaccharide synthesis in the model diatom, phaeodactylum tricornutum†

Abstract: The effects of phosphate (P) limitation, varying salinity (5-65 psu), and solid media growth conditions on the polysaccharides produced by the model diatom, Phaeodactylum tricornutum Bohlin were determined. Sequential extraction was used to separate polymers into colloidal (CL), colloidal extracellular polymeric substances (cEPS), hot water soluble (HW), hot bicarbonate soluble (HB), and hot alkali (HA) soluble fractions. Media-soluble polymers (CL and cEPS) were enriched in 4-linked mannosyl, glucosyl, and galactosyl residues as well as terminal and 3-linked xylosyl residues, whereas HW polymers consisted mainly of 3-linked glucosyl as well as terminal and 2,4-linked glucuronosyl residues. The HB fraction was enriched in terminal and 2-linked rhamnosyl residues derived from the mucilage coating solubilized by this treatment. Hot alkali treatment resulted in the complete dissolution of the frustule, releasing polymers containing 2,3- and 3-linked mannosyl residues. The fusiform morphotype predominated in standard and P-limited cultures and cultures subjected to salinity variations, but growth on solid media resulted in an enrichment of the oval morphotype. The proportion and linkages of 15 residues, including neutral, uronic acid, and O-methylated sugars, varied with environmental conditions. P limitation and salinity changes resulted in 1.5- to 2.5-fold increase in carbohydrate production, with enrichment of highly branched/substituted and terminal rhamnose, xylose, and fucose as well as O-methylated sugars, uronic acids, and sulfate. The increased deoxy- and O-methylated sugar content under unfavorable environments enhances the hydrophobicity of the polymers, whereas the anionic components may play important roles in ionic cross-linking, suggesting that these changes could ameliorate the effects of salinity or P-stress and that these altered polysaccharide characteristics may be useful as bioindicators for environmental stress.

Optimal waveform design for UWB radios

Abstract: With transmit power spectra strictly limited by regulatory spectral masks, the emerging ultra-wideband (UWB) communication systems call for judicious pulse shape design in order to achieve optimal spectrum utilization, spectral mask compatibility, and coexistence with other wireless services. Meanwhile, orthogonal pulse sets are often desired in order to apply high-rate multidimensional modulation and (carrier-free) orthogonal frequency-division multiple access. Motivated by these considerations, we suggest a digital finite impulse response (FIR) filter approach to synthesizing UWB pulses and propose filter design techniques by which optimal waveforms that satisfy the spectral mask can be efficiently obtained. For single pulse design, we develop a convex formulation for the design of the FIR filter coefficients that maximize the spectrum utilization efficiency in terms of both the bandwidth and power allowed by the spectral mask. For orthogonal pulse design, a sequential strategy is derived to formulate the overall pulse design problem as a set of convex subproblems, which are then solved in a sequential manner to yield a set of mutually orthogonal pulses. Our design techniques not only provide waveforms with high spectrum utilization and guaranteed spectral mask compliance but also permit simple modifications that can accommodate several other system objectives.

An experimental comparison between several active composite actuators for power generation

Abstract: The use of piezoelectric materials for power harvesting has attracted significant interest over the past few years. The majority of research on this subject has sought to quantify the amount of energy generated in power harvesting applications, or to develop methods of improving the amount of energy generated. Usually, a monolithic piezoelectric material with a traditional electrode pattern and poled through its thickness is used for power harvesting. However, in recent years several companies and research institutions have begun to develop and market a broad range of piezoelectric composite sensor/actuator packages, each conceived for specific operational advantages and characteristics. Commonly, these devices are employed in control and vibration suppression applications, and their potential for use in power-harvesting systems remains largely unknown. Two frequently implemented design techniques for improving the performance of such actuators are the use of interdigitated electrodes and piezofibers. This paper seeks to experimentally quantify the differences in performance in power-harvesting applications between several of these new actuators and to identify the reasons for their relative performance characteristics. A special focus on the structural and compositional differences between each actuator is incorporated in the discussion of the effectiveness of each actuator as a power-harvesting device.

Effects of Cell Shape and Strut Cross-Sectional Area Variations on the Elastic Properties of Three-Dimensional Open-cell Foams

Abstract: The Voronoi tessellation technique and the finite element (FE) method are utilized to investigate the microstructure–property relations of three-dimensional (3-D) cellular solids (foams) that have irregular cell shapes and non-uniform strut cross-sectional areas (SCSAs). Perturbations are introduced to a regular packing of seeds to generate a spatially periodic Voronoi diagram with different degrees of cell shape irregularity (amplitude a ), and to the constant SCSA to generate a uniform distribution of SCSAs with different degrees of SCSA non-uniformity (amplitude b ). Twenty FE models are constructed, based on the Voronoi diagrams for twenty foam samples (specimens) having the same pair of a and b , to obtain the mean values and standard deviations of the elastic properties. Spatially periodic boundary conditions are applied to each specimen. The simulation results indicate that for low-density imperfect foams, the elastic moduli increase as cell shapes become more irregular, but decrease as SCSAs get less uniform. When the relative density ( R ) increases, the elastic moduli of imperfect foams increase substantially, while the Poisson's ratios decrease moderately. The effect of the interaction between the two types of imperfections on foam elastic properties appears to be weak. In addition, it is found that the strut cross-sectional shape has a significant effect on the foam properties. Also, the elastic response of foams with the cell shape and SCSA imperfections appears to be isotropic regardless of changes in a , b and R and the strut cross-sectional shape.

Transgenic modification of gai or rgl1 causes dwarfing and alters gibberellins, root growth, and metabolite profiles in Populus

Abstract: In Arabidopsis and other plants, gibberellin (GA)-regulated responses are mediated by proteins including GAI, RGA and RGL1-3 that contain a functional DELLA domain. Through transgenic modi- fication, we found that DELLA-less versions of GAI (gai) and RGL1 (rgl1) in a Populus tree have profound, dominant effects on phenotype, producing pleiotropic changes in morphology and metabolic profiles. Shoots were dwarfed, likely via constitutive repression of GA- induced elongation, whereas root growth was promoted two- to threefold in vitro. Applied GA3 inhibited adventitious root production in wild-type poplar, but gai/rgl1 poplars were unaffected by the inhibition. The concentrations of bioactive GA1 and GA4 in leaves of gai- and rgl1-expressing plants increased 12- to 64-fold, while the C19 precursors of GA1 (GA53 ,G A 44 and GA19) decreased three- to ninefold, consistent with feedback regulation of GA 20-oxidase in the transgenic plants. The transgenic modifications elicited significant metabolic changes. In roots, metabolic profiling sug- gested increased respiration as a possible mechanism of the increased root growth. In leaves, we found meta- bolite changes suggesting reduced carbon flux through the lignin biosynthetic pathway and a shift towards allocation of secondary storage and defense metabolites, including various phenols, phenolic glucosides, and phenolic acid conjugates.

Benthic diatoms as indicators of eutrophication in tropical streams

Abstract: Diatoms are frequently used as indicators of eutrophication in temperate systems, but little is known about their application to impacted African tropical systems. Five streams located within Gombe Stream National Park and five streams supporting human settlements draining into Lake Tanganyika, East Africa, were investigated for species composition, richness and diversity of epilithic algae. In addition, a trophic diatom index (TDI) developed for monitoring European rivers was applied to these tropical systems. 54 specific and infraspecific diatom taxa representing 20 genera were identified for all sites with Achnanthes s.l., Gomphonema and Navicula s.l. being the most common genera. Species richness varied between 10 and 21 in disturbed streams and 13 and 19 in undisturbed streams. Nutrients were significantly enriched in streams draining the deforested watersheds but indices of diversity and evenness (Shannon H, J and Simpson–Yule D, E) did not show any significant differences between streams in forested and deforested watersheds. Significant differences were observed between pooled data for the TDI between forested and deforested watersheds. Analysis of percent pollution tolerant diatom taxa indicates that organic pollution of streams in deforested watersheds may be contributing to eutrophication. This study shows that African diatoms, cosmopolitan or resembling well-known North American and European taxa, allows for trophic indices tailored to the autecological preferences of species to be applied to new regions, although intensive studies on these African taxa will lead to more accurate results. Measures of species-richness and diversity, historically used to describe the state of an ecosystem, may not be suitable to evaluate streams which are not grossly polluted.

Ozone production from the 2004 North American boreal fires

Abstract: We examine the ozone production from boreal forest fires based on a case study of wildfires in Alaska and Canada in summer 2004 The model simulations were performed with the chemistry transport model, MOZART-4, and were evaluated by comparison with a comprehensive set of aircraft measurements In the analysis we use measurements and model simulations of carbon monoxide (CO) and ozone (O3) at the PICO-NARE station located in the Azores within the pathway of North American outflow The modeled mixing ratios were used to test the robustness of the enhancement ratio deltaO3/deltaCO (defined as the excess O3 mixing ratio normalized by the increase in CO) and the feasibility for using this ratio in estimating the O3 production from the wildfires Modeled and observed enhancement ratios are about 025 ppbv/ppbv which is in the range of values found in the literature, and results in a global net O3 production of 129 2 Tg O3 during summer 2004 This matches the net O3 production calculated in the model for a region extending from Alaska to the East Atlantic (9-11 Tg O3) indicating that observations at PICO-NARE representing photochemically well-aged plumes provide a good measure of the O3 production of North American boreal fires However, net chemical loss of fire related O3 dominates in regions far downwind from the fires (eg Europe and Asia) resulting in a global net O3 production of 6 Tg O3 during the same time period On average, the fires increased the O3 burden (surface-300 mbar) over Alaska and Canada during summer 2004 by about 7-9%, and over Europe by about 2-3%

Selection of Northern Yellowstone Elk by Gray Wolves and Hunters

Abstract: We compared selection of northern Yellowstone elk (Cervus elaphus) by hunters in the Gardiner Late Hunt and northern Yellowstone wolves (Canis lupus) with regard to sex, age, and impacts to recruitment. We compared harvest data from 1996–2001 with wolf-killed elk data from 1995–2001. We assessed the effects of hunting and wolf predation on reproductive female elk by constructing a life table and calculating reproductive values for females in the northern Yellowstone herd. We devised an index of total reproductive impact to measure impacts to calf production due to hunting and wolf predation. The age classes of female elk selected by wolves and hunters were significantly different. Hunters selected a large proportion of female elk with the greatest reproductive values, whereas wolves selected a large proportion of elk calves and older females with low reproductive values. The mean age of adult females killed by hunters throughout the study period was 6.5 years, whereas the mean age of adult females killed by wolves was 13.9 years. Hunting exerted a greater total reproductive impact on the herd than wolf predation. The combined effects of hunters killing prime-aged females (2–9 yr old), wolves killing calves, and predation by other predators has the potential to limit the elk population in the future. Yellowstone is unique in this regard because multiple predators that occur sympatrically, including hunters, wolves, grizzly bears (Ursus arctos), black bears (Ursus americanus), cougars (Felis concolor), and coyotes (Canis latrans), all prey on elk. Using an Adaptive Harvest Management process the known female elk harvest during the Gardiner Late Hunt has been reduced by 72% from 2,221 elk in 1997 to 620 elk in 2004. In the future, hunting harvest levels may be reduced further to partially offset elk losses to wolves, other predators, and environmental factors.