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Recent documents in eScholarship Repository

  • Environmental Assessment and Metrics for Solar: Case Study of SolFocus Solar Concentrator Systems
    Life-cycle assessment (LCA) is utilized to analyze SolFocus Inc. concentrator solar systems. A hybrid LCA methodology is explained that combines process and input-output LCA techniques. The use of the greenhouse gas return on investment metric for solar technologies is discussed as a complement to energy metrics. Finally, preliminary results of a hybrid LCA for the SolFocus concentrator technology are presented. It is found that transportation and electricity consumption play a significant role in energy consumption and greenhouse gas emissions.

  • Environmental Performance Characterization of Atomic Layer Deposition
    Atomic Layer Deposition (ALD) is emerging as a promising nanotechnology for manufacturing dielectrics and insulators on microelectronics devices. Its environmental performance has to be characterized at this early development stage to achieve sustainable manufacturing in the future. In this paper, we report our environmental performance characterization studies on ALD technology through material flow analysis and energy flow analysis. The assessed ALD process is for deposition of Al2O3 high-k dielectric films on a 4 inch silicon wafer. The results show that only 50.4% of input Trimethyl Aluminum (TMA) material is turned into Al2O3 film, while the other half is transformed into toxic emissions into the environment. Material usage efficiency of water is only 2.03% in current ALD processes. ALD is also featured with intensive energy consumption. For the studied ALD process, a total of 4.09 MJ energy is consumed for deposition of a 30 nm Al2O3 film, with averaged energy consumption at 13.6 KJ per cycle.

  • Modeling and Simulations of the Spawning Migration of Pelagic Fish
    We model the spawning migration of the Icelandic capelin stock using an interacting particle model with added environmental fields. Without artificial forcing terms or a homing instinct, we qualitatively reproduce several observed spawning migrations using available temperature data and approximated currents. The simulations include orders of magnitude more particles than many similar models, affecting the global behavior of the system. Without environmental fields, we analyze how various parameters scale with the number of particles. In particular we present scaling behavior between the size of the time step, radii of the sensory zones and the number of particles in the system. We then discuss incorporating environmental data into the model.

  • The Cell Phone and the Crowd: Messianic Politics in the Contemporary Philippines
    This essay explores the role of the cell phones and the practice of texting within the context of the civilian backed coup that overthrew President Joseph Estrada in January of 2001 popularly known as "People Power II." It focuses in particular on a set of political fantasies among the Filipino middle class, including their belief in in the power of communication technologies to transmit messages at a distance and in their ability to possess that power. In the same vein, they had faith in their ability to master their relationship to the masses of people with whom they regularly shared Manila's crowded streets, utilizing the power of crowds to speak to the state. Communication from this perspective held the messianic promise of refashioning the heterogenous crowd into a people addressing and addressed by the promise of justice. But as we shall see, such telecommunicative notions were predicated on the putative "voicelessness" of the masses. For once heard, the masses called attention to the fragility of bourgeois claims to shape the sending and reception of messages about the proper practice of politics in the nation-state.

  • Role of Fencing in Promoting Wildlife Underpass Use and Highway Permeability
    Ungulate-proof fencing has been used successfully to mitigate the incidence of wildlife-vehicle collisions on highways throughout North America. And while fencing is often regarded as an integral component of effective wildlife passage structures, limited information or guidelines exist for the application of fencing in conjunction with wildlife passages. Fencing itself may limit wildlife permeability across highways and exacerbate the barrier effect of highways on wildlife populations. An 8-km section of highway reconstructed from a two- to four-lane divided highway in central Arizona was opened to traffic six months before ungulate-proof fencing was erected linking four wildlife underpasses (UP) and three bridges. To assess the role of strategically placed fencing along 49% of the section, we compared before and after fencing Rocky Mountain elk (Cervus elaphus nelsoni)-vehicle collision incidence, wildlife use of UP, and elk highway permeability. From 2002-2006, we documented 110 elk-vehicle collisions. The incidence of collisions increased over three fold after highway reconstruction was completed but before fencing was erected. After fencing, the incidence of elk collisions declined 87%. We employed video camera surveillance systems at two UP to compare wildlife use for nine months before and 11 months after fencing was erected. Before fencing, we recorded 500 elk and deer (Odocoileus spp.) at the UP, of which only 12% successfully passed through the UP; 81% of animals continued to cross the highway at grade. After fencing, of 595 elk and deer recorded, 56% crossed successfully and no animals crossed the highway at grade. The probability of an approaching animal crossing through an UP increased from 0.09 to 0.56 with fencing, and the combined odds of a crossing through the UP after fencing was 13.6:1 compared to before fencing. We used Global Positioning System (GPS) telemetry to assess highway permeability and crossing patterns. We instrumented 22 elk (16 female, 6 male) with GPS receiver collars April 2004-October 2005, during which time our collars accrued 87,745 GPS fixes. The elk highway passage rate, our measure of permeability, after the highway was opened to traffic but before fencing was erected (0.54 crossings/approach) was 32% lower than the level determined from a previous study for the section during reconstruction (0.79 crossings/approach). Once fencing was erected, the passage rate increased 52% to 0.82 crossings/approach. The proportion of elk crossings that occurred along fenced highway stretches declined 50% while the proportion of crossings along unfenced highway increased 40%. Fencing plays an important role in reducing the incidence of wildlife-vehicle collisions and increasing the effectiveness of wildlife passage structures. Furthermore, fencing in combination with a relatively high density of passages (1 struc¬ture/1.1 km) promoted elk highway permeability by funneling animals toward the UP where resistance to crossing was lower than that associated with crossings at grade.

  • Process Design for Collaboration: An Innovative Approach to Redesigning the Environmental Review Process for Transportation Projects
    Project Overview: Recent federal legislation and accompanying rules (SAFETEA-LU) require state Departments of Transportation to increase their levels of collaboration with local jurisdictions and with other state and federal environ¬mental and resource agencies related to the environmental impact of transportation projects. At the same time, they face increased demands for reducing the time and cost associated with project environmental reviews and permitting. Some barriers to achieving these desired results, experienced by DOTs, are: Misunderstanding of goals, priorities and expectations among the DOT, local jurisdictions, and resource/regula¬tory agencies during project development. Items and requests passed from one agency to another getting "lost in the shuffle." Duplication of effort to gather and assess environmental data by the DOT, local planning agencies (MPOs), community organizations, and resource agencies. Important environmental or community impact considerations arising late in project development/delivery process, creating unexpected costs and schedule delays. Choice of a project alternative by the MPO that requires very costly and time consuming environmental studies and mitigation efforts. Frequent rework of environmental documents and delays in study and permit approvals.The Language-Action Framework focuses on building commitments and coordination between customers (for example, a DOT that needs a water resource study) and performers (for example, a consultant who completes the water resource study). This approach provides a structure for improving coordination using the following key communication points: a. Clear and specific statements of customer needs, including the motivation for the proposed effort b. Agreement between customer and provider on cycle time, cost and quality expectations for the work, so that there is a shared understanding of and commitment to meeting these expectations. c. Progress tracking and reporting, so that needed mid-course adjustments can be made in schedule, budget or other areas of the project d. Interim customer feedback on project deliverables e. Report of completed work to the customer f. Customer review, assessment and feedback on work delivered, and recommendations for continuous quality improvement which are developed collaboratively by customer and performer.Sample process designs have been developed, using the Language Action Framework, for three key process areas: integrating long range planning with the NEPA process, coordinating resource and regulatory agency review of environ¬mental decisions and documents (EIS or EA), and ensuring the fulfillment of environmental commitments (including mitigation or other measures). These process designs, when adapted to the unique situation and needs of a particular agency, show potential for a wide range of tangible benefits, including: Reduced time and effort to produce environmental documents (EAs and EISs). Improved relationships between DOTs and the various resource, regulatory, and local jurisdiction agencies they collaborate with to produce and obtain approval for environmental documents. Increased clarity about roles and accountabilities for completing environmental studies among DOT staff, the DOT's partner agencies, and consultants/contractors. Improved reliability of the DOT's project schedules. Improved environmental outcomes, achieved through greater clarity and broad interagency commitment regard¬ing those outcomes. List of current/anticipated results: The Language-Action Framework has been used to design a set of sample diagrams and descriptions for typical DOT environmental streamlining processes. These process designs reflect the experience of TDOT, as well as recent AASHTO and FHWA studies of environmental streamlining and environmental management system processes within DOTs. Recommendations for future research: This approach should be further tested by DOTs of various sizes and in various parts of the country, for its viability and application to meet their environmental streamlining and stewardship needs. The approach may also improve collaboration and coordination for specific environmental mitigations or other actions--for example, multi-agency coordination

  • Integrating Wildlife Crossing into Transportation Plans and Projects in North America
    Results are presented of a North American survey designed to learn how transportation departments mitigate transportation corridors for wildlife and give examples of how wildlife mitigation measures can be incorpo¬rated into long range plans and in routine everyday actions. The objective is to promote greater understanding of the potential for incorporating wildlife movement needs into transportation programs and projects. Research results presented include data from a continent-wide telephone survey conducted over a two year period (2004-2006) to learn of accomplishments in wildlife passage and how wildlife and ecosystem needs have been incorporated into the trans¬portation planning process. Telephone interviews were conducted with 410 transportation and ecology professionals in every state and province. Based on research data and the mandates of the SAFETEA-LU legislation the case is made that greater efforts in long term transportation plans and everyday retrofits are necessary to provide for wildlife and ecosystems needs. Some efforts have already been accomplished and can be adapted continent-wide. There are greater than 580 terrestrial and 10,000 aquatic wildlife and fish passages in North America that were specifically built as wildlife and fish crossings, and millions of other bridges and culverts constructed for other purposes but which could be used by wildlife. Placement of these structures has grown so rapidly that over 500 new terrestrial passages are projected to be built in the next 10 years. The almost exponential increase in passage construction each decade is an indication of the growing awareness of the need to mitigate new and existing transportation infrastructure for wildlife permeability. There is also a greater awareness that early planning for wildlife and ecosystems is critical to accomplish these mitigation activities. The inclusion of wildlife and ecosystem needs early in the development of long range transportation plans has not been the traditional paradigm as was learned over the course of the survey. The majority of transportation planners who participated in the survey indicated their state's consideration of wildlife and ecosystems, in the form of consultations with natural resource professionals and referencing Geographic Information Systems (GIS) maps and other data, did not occur until the project development stage. This late consideration does not typically allow adequate time to avoid important wildlife corridors and to install mitigation measures. The majority of those working with transportation and ecological concerns recognized the need to incorporate wildlife mitigation needs early in the programming, planning, and design processes, as learned from the web-based priorities survey. The survey revealed that early planning for wildlife and ecosystem needs was the number one priority in dealing with roads and wildlife. This early level planning has also been mandated in the U. S. SAFETEA-LU Transportation Act of 2005. Examples are presented of instances where long range planning included wildlife and ecosystems needs, and suggest how this can be accomplished on a state and province-wide basis. We also present how everyday opportunities can be used to facilitate wildlife movement over and under roads and railways. Knowledge of successful accomplishments can help build upon opportunities in the movement toward a more proactive transportation planning paradigm.

  • Patch Occupancy Models and Black Bear Management in the Southeastern Coastal Plain: A Potential Tool?
    Habitat fragmentation in the southeastern Coastal Plain is widely regarded as a central issue in the management of black bear (Ursus americanus) populations. Further habitat loss and fragmentation, and increases in human density, may influence the persistence of black bears throughout this region. Therefore, tools to evaluate these impacts are needed to encourage and allow for an integrated, regional-scale approach to management. Stochastic patch occu¬pancy models (SPOMs) represent a group of metapopulation models that are based only on the occupancy status and size and distribution (i.e., connectivity) of habitat patches. Application of such models may provide wildlife managers and landscape planners with useful tools to evaluate the potential impacts of future land-use changes (e.g., construc¬tion of new highways) on the persistence of wildlife populations at a regional scale and to determine how those impacts may be mitigated (e.g., establishing corridors). We developed a SPOM for the area encompassing the entire range of the Florida black bear (U. a. floridanus) and applied the model to quantify colonization and extinction rates of habitat patches across the network. We adjusted interpatch distances using least-cost distance analyses to account for char¬acteristics of the landscape (i.e., roads and land-cover types) and their potential effects on dispersal among patches. The best-fitting model incorporated effects of land-cover type and roads, including type of road. Using the parameter estimates of the best model, we performed a 25-year simulation of patch incidence to assess the potential for natural recolonization of unoccupied patches and to identify patches that may become extinct over the 25-year period. The simulation predicted only limited population expansion but also predicted low potential for extinction, thus occupancy patterns exhibited high stability. To demonstrate the potential utility of our model to managers and landscape planners, we applied our models to hypothetical management scenarios. We demonstrated how our model could be used to guide restoration efforts by identifying those patches within an assemblage that, if restocked, would maximize recolo¬nization potential for surrounding patches. We also demonstrated how our model could be used to assess impacts on connectivity among existing bear populations resulting from changes in landscape structure and composition (e.g., highway upgrades). Additionally, we applied the parameter estimates of the best model, tested the validity of its ap¬plication, and performed simulations for the area encompassing the entire range of the federally threatened Louisiana black bear (U. a. luteolus) and populations of the American black bear (U. a. americanus) in Arkansas. Although SPOMs may prove to be a valuable tool for regional-scale management of black bears in the southeastern Coastal Plain, we caution that the methodology used to develop our model has not been attempted for large carnivores and the reliability of our predictions has not been thoroughly tested. Thus, we emphasize that our model should be used in conjunction with other available information and not provide the sole basis for making management decisions.

  • Using Matrix Models to Evaluate Abalone Conservation and Fishery
    The objectives of the project were to create practical quantitative tools to address applied fishery management and marine conservation problems for California's abalone populations. We accomplished both goals during this project.

  • Characterization of selective binding of alkali cations with carboxylate by x-ray absorption spectroscopy of liquid microjets
    We describe an approach for characterizing selective binding between oppositely charged ionic functional groups under biologically relevant conditions. Relative shifts in K-shell x-ray absorption spectra of aqueous cations and carboxylate anions indicate the corresponding binding strengths via perturbations of carbonyl antibonding orbitals. XAS spectra measured for aqueous formate and acetate solutions containing lithium, sodium, and potassium cations reveal monotonically stronger binding of the lighter metals, supporting recent results from simulations and other experiments. The carbon K-edge spectra of the acetate carbonyl feature centered near 290 eV clearly indicate a preferential interaction of sodium versus potassium, which was less apparent with formate. These results are in accord with the Law of Matching Water Affinities, relating relative hydration strengths of ions to their respective tendencies to form contact ion pairs. Density functional theory calculations of K-shell spectra support the experimental findings.

  • Translating the cancer genome: Going beyond p values


  • (2,2-Bipyridyl)bis(eta5-1,2,3,4,5-pentamethylcyclopentadienyl)Strontium(II)


  • Recirculation in multiple wave conversions


  • Integrated Ecogenomics Study for Bioremediation of Cr(VI) at Hanford 100H Area
    Hexavalent chromium is a widespread contaminant found in groundwater. In order to stimulate microbially mediated Cr(VI)-reduction, a poly-lactate compound was injected into Cr(VI)-contaminated aquifers at site 100H at Hanford. Investigation of bacterial community composition using high-density DNA microarray analysis of 16S rRNA gene products revealed a stimulation of Pseudomonas, Desulfovibrio and Geobacter species amongst others. Enrichment of these organisms coincided with continued Cr(VI) depletion. Functional gene-array analysis of DNA from monitoring well indicated high abundance of genes involved in nitrate-reduction, sulfate-reduction, iron-reduction, methanogenesis, chromium tolerance/reduction. Clone-library data revealed Psedomonas was the dominant genus in these samples. Based on above results, we conducted lab investigations to study the dominant anaerobic culturable microbial populations present at this site and their role in Cr(VI)-reduction. Enrichments using defined anaerobic media resulted in isolation of an iron-reducing, a sulfate-reducing and a nitrate-reducing isolate among several others. Preliminary 16S rDNA sequence analysis identified the isolates as Geobacter metallireducens, Pseudomonas stutzeri and Desulfovibrio vulgaris species respectively. The Pseudomonas isolate utilized acetate, lactate, glycerol and pyruvate as alternative carbon sources, and reduced Cr(VI). Anaerobic washed cell suspension of strain HLN reduced almost 95?M Cr(VI) within 4 hr. Further, with 100?M Cr(VI) as sole electron-acceptor, cells grew to 4.05 x 107 /ml over 24 h after an initial lag, demonstrating direct enzymatic Cr(VI) reduction coupled to growth. These results demonstrate that Cr(VI)-immobilization at Hanford 100H site could be mediated by direct microbial metabolism in addition to indirect chemical reduction of Cr(VI) by end-products of microbial activity.

  • Design and Test of a Nb3Sn Subscale Dipole Magnet for Training Studies


  • Quantum Dynamical Behaviour in Complex Systems - A Semiclassical Approach
    One of the biggest challenges in Chemical Dynamics is describing the behavior of complex systems accurately. Classical MD simulations have evolved to a point where calculations involving thousands of atoms are routinely carried out. Capturing coherence, tunneling and other such quantum effects for these systems, however, has proven considerably harder. Semiclassical methods such as the Initial Value Representation (SC-IVR) provide a practical way to include quantum effects while still utilizing only classical trajectory information. For smaller systems, this method has been proven to be most effective, encouraging the hope that it can be extended to deal with a large number of degrees of freedom. Several variations upon the original idea of the SCIVR have been developed to help make these larger calculations more tractable; these range from the simplest, classical limit form, the Linearized IVR (LSC-IVR) to the quantum limit form, the Exact Forward-Backward version (EFB-IVR). In this thesis a method to tune between these limits is described which allows us to choose exactly which degrees of freedom we wish to treat in a more quantum mechanical fashion and to what extent. This formulation is called the Tuning IVR (TIVR). We further describe methodology being developed to evaluate the prefactor term that appears in the IVR formalism. The regular prefactor is composed of the Monodromy matrices (jacobians of the transformation from initial to finial coordinates and momenta) which are time evolved using the Hessian. Standard MD simulations require the potential surfaces and their gradients, but very rarely is there any information on the second derivative. We would like to be able to carry out the SC-IVR calculation without this information too. With this in mind a finite difference scheme to obtain the Hessian on-the-fly is proposed. We also apply the IVR formalism to a few problems of current interest. A method to obtain energy eigenvalues accurately for complex systems is described. We proposed the use of a semiclassical correction term to a preliminary quantum calculation using, for instance, a variational approach. This allows us to increase the accuracy significantly. Modeling Nonadiabatic dynamics has always been a challenge to classical simulations because the multi-state nature of the dynamics cannot be described accurately by the time evolution on a single average surface, as is the classical approach. We show that using the Meyer-Miller-Stock-Thoss (MMST) representation of the exact vibronic Hamiltonian in combination with the IVR allows us to accurately describe dynamics where the non Born-Oppenheimer regime. One final problem that we address is that of extending this method to the long time regime. We propose the use of a time independent sampling function in the Monte Carlo integration over the phase space of initial trajectory conditions. This allows us to better choose the regions of importance at the various points in time; by using more trajectories in the important regions, we show that the integration can be converged much easier. An algorithm based loosely on the methods of Diffusion Monte Carlo is developed that allows us to carry out this time dependent sampling in a most efficient manner.

  • Monochromatic electron photoemission from diamondoid monolayers
    We found monochromatic electron photoemission from large-area self-assembled monolayers of a functionalized diamondoid, [121]tetramantane-6-thiol. Photoelectron spectra of the diamondoid monolayers exhibited a peak at the low-kinetic energy threshold; up to 68percent of all emitted electrons were emitted within this single energy peak. The intensity of the emission peak is indicative of diamondoids being negative electron affinity materials. With an energy distribution width of less than 0.5 electron volts, this source of monochromatic electrons may find application in technologies such as electron microscopy, electron beam lithography, and field-emission flatpanel displays.

  • High-resolution detection system for time-of-flight electron spectrometry
    One of the key components of a time-of-flight (TOF) spectrometer is the detection system. In addition to high timing resolution, accurate two-dimensional imaging substantially broadens the areas of applications of TOF spectrometers; for example, add a new dimension to angle-resolved photoemission spectroscopy (ARPES). In this paper we report on the recent developments of a high spatial (<50 mm) and timing (<130 ps) resolution imaging system capable of selective detection of electrons, ions and/or photons. Relative to our previously reported results, we have substantially improved the counting rate capabilities of the system especially for cases where the energy range of interest represents a small fraction of the incoming flux at the detector plane. The new system ignores all the events outside of a tunable time window substantially decreasing the dead time required for the event processing. That allows high-resolution TOF measurements within a given energy or momentum range and also can be used for distinguishing (or disabling) detection of photons versus detection of charged particles. The counting rate within a given energy window can be as high as ~;;400KHz at 10percent dead time. The electron detection system reported in the paper was developed for the TOF ARPES experiments at the Advanced Light Source, Lawrence Berkeley National Laboratory.

  • Complete momentum and energy resolved TOF electron spectrometer for time-resolved photoemission spectroscopy
    Over the last decade, high-resolution Angle-Resolved Photoemission Spectroscopy (ARPES) has emerged as a tool of choice for studying the electronic structure of solids, in particular, strongly correlated complex materials such as cuprate superconductors. In this paper we present the design of a novel time-of-flight based electron analyzer with capability of 2D in momentum space (kx and ky) and all energies (calculated from time of flight) in the third dimension. This analyzer will utilize an improved version of a 2D delay line detector capable of imaging with <35 mm (700x700 pixels) spatial resolution and better than 120 ps FWHM timing resolution. Electron optics concepts and optimization procedure are considered for achieving an energy resolution less than 1 meV and an angular resolution better than 0.11.

  • The Effects of Various Conductive Additive and Polymeric Binder Contents on the Performance of a Lithium-ion Composite


  • Diffusion-controlled spherulite growth in obsidian inferred from H2O concentration profiles
    Spherulites are spherical clusters of radiating crystals that occur naturally in rhyolitic obsidian. The growth of spherulites requires diffusion and uptake of crystal forming components from the host rhyolite melt or glass, and rejection of non-crystal forming components from the crystallizing region. Water concentration profiles measured by synchrotron-source Fourier transform spectroscopy reveal that water is expelled into the surrounding matrix during spherulite growth, and that it diffuses outward ahead of the advancing crystalline front. We compare these profiles to models of water diffusion in rhyolite to estimate timescales for spherulite growth. Using a diffusion-controlled growth law, we find that spherulites can grow on the order of days to months at temperatures above the glass transition. The diffusion-controlled growth law also accounts for spherulite size distribution, spherulite growth below the glass transition, and why spherulitic glasses are not completely devitrified.

  • Dirac charge dynamics in graphene by infrared spectroscopy
    A remarkable manifestation of the quantum character of electrons in matter is offered by graphene, a single atomic layer of graphite. Unlike conventional solids where electrons are described with the Schrödinger equation, electronic excitations in graphene are governed by the Dirac hamiltonian. Some of the intriguing electronic properties of graphene, such as massless Dirac quasiparticles with linear energy-momentum dispersion, have been confirmed by recent observations. Here, we report an infrared spectromicroscopy study of charge dynamics in graphene integrated in gated devices. Our measurements verify the expected characteristics of graphene and, owing to the previously unattainable accuracy of infrared experiments, also uncover significant departures of the quasiparticle dynamics from predictions made for Dirac fermions in idealized, free-standing graphene. Several observations reported here indicate the relevance of many-body interactions to the electromagnetic response of graphene.

  • Formation mechanism and properties of CdS-Ag2S nanorod superlattices


  • Hierarchy of multiple many-body interaction scales in high-temperature superconductors


  • Effects of d-electrons in pseudopotential screened-exchange density functional calculations


  • In-Situ observation of wet oxidation kinetics on Si (100) via ambient pressure x-ray photoemission spectroscopy


  • Distributed Generation Investment by a Microgrid under Uncertainty
    This paper examines a California-based microgrid?s decision to invest in a distributed generation (DG) unit fuelled by natural gas. While the long-term natural gas generation cost is stochastic, we initially assume that the microgrid may purchase electricity at a fixed retail rate from its utility. Using the real options approach, we find a natural gas generation cost threshold that triggers DG investment. Furthermore, the consideration of operational flexibility by the microgrid increases DG investment, while the option to disconnect from the utility is not attractive. By allowing the electricity price to be stochastic, we next determine an investment threshold boundary and find that high electricity price volatility relative to that of natural gas generation cost delays investment while simultaneously increasing the value of the investment. We conclude by using this result to find the implicit option value of the DG unit when two sources of uncertainty exist.

  • The structure of a-C: What NEXAFS and EXAFS see
    Mechanically hard ha-C and soft sa-C amorphous carbon films of 2.9 and 2.2 g cm-3 approximate densities were prepared by filtered cathodic arc deposition and analyzed by near-edge x-ray absorption spectroscopy NEXAFS and extended x-ray absorption spectroscopy EXAFS to determine their structure. The analysis observed an insignificant level of pi bond conjugation in both kind of films. EXAFS distinguished two types of atomic environments in them: one semiordered with well defined bond lengths, and the other with so strong bond disorder that its contribution to EXAFS was undetectable. The proportion of atoms in the semiordered atomic environments was of less than 40percent in both films. Their bond lengths were similar to those of diamond in the ha-C films and to graphite in the sa-C. NEXAFS spectra analysis was based on the linear relation between sigma* energy and bond length. It served to quantify the proportion of sp3 bonded atoms in a-C, to deduce the average bond length of the atoms undetected by EXAFS, and to determine the level of bond conjugation in the films. The sp3 concentration estimated with the proposed method was of 44percent in the ha-C films and 10percent in the sa-C films. These values were consistent with the EXAFS results, but disagreed with those obtained based on the traditional pi*/sigma* intensity ratio method which overestimated sp3 concentrations. Annealing of the ha-C films up to its almost complete graphitization caused a gradual reduction in bond length of the semiordered environments with no differentiation between two phases, diamondlike and graphitelike, at any temperature. This result support models that explain sp3 bond promotion in a-C as caused by the high compressive stress attained by a strongly disordered sp2 dense structure during film deposition.

  • Simulation and Analysis of Microwave Transmission through an Electron Cloud, a Comparison of Results
    Simulation studies for transmission of microwaves through electron cloudes show good agreement with analytic results. The elctron cloud produces a shift in phase of the microwave. Experimental observation of this phenomena would lead to a useful diagnostic tool for acessing the local density of electron clouds in an accelerator. These experiments are being carried out at the CERN SPS and the PEP-II LER at SLAC and is proposed to be done at the Fermilab maininjector. In this study, a brief analysis of the phase shift is provided and the results are compared with that obtained from simulations.

  • Complete fabrication of target experimental chamber and implement initial target diagnostics to be used for the first target experiments in NDCX-1


  • Wildlife Vehicle Collision be Decreased by Increasing the Number of Wildlife Passages in Korea?
    The mitigation of fragmentation due to high density road network has been a hot topic among environmentalistsand road construction engineers of South Korea. Over the last ten years 92 wildlife passages, 55 ecoducts and 37 wildlife underpasses, have been constructed on existing roads, and many more will be constructed in the future (Ministry of Environment of the Republic of Korea, 2006). We are at an early stage of data collection on wildlife vehicle collision and the role of traditionally non-wildlife-engineered passages, such as underpasses including bridges, culverts, and human underpasses, for wildlife passages.The objective of this study was to analyze the effectiveness of the number, size, and density of non-wildlife-engineered passages. This study employed three monitoring methods: wildlife vehicle collisions, the passages use ratio (Servheen, 2003) and radio telemetry. The effectiveness of such unintended wildlife passage was evaluated by using the relationship between monthly wildlife vehicle collision data, number of usable passages, use rate of passages, and passage density.The number of usable passages represents all crossing structures after excluding those inundated circular culverts during summer season, since they are impassable for most wildlife species. The use rates of wildlife passages were collected from 14 underpasses. They were seven circular culverts, two box culverts, and four human underpasses, and were selected from 31 structures constructed on a 6.6km segment of a four-lane highway. The landscape of study area mainly consists of rice fields on an alluvial plane and scattered forest, and the road runs along the stream. Every passage has similar surroundings. Wildlife monitoring was carried out for 12 months, from Sept. 2005 to Aug. 2006; using camera traps (an average of 239 camera operating days). The number of recorded mammals was 2,593, consisting of 13 species. We also documented 93 mammal vehicle collisions comprising 12 species by monitoring the same road daily over a period of two years (Sept. 2004-Aug. 2006).The results of our analysis are as follows. First, the use rate of passages and the number of mammal vehicle collisions showed a positive correlation (r=0.890). Second, the fluctuation of the number of usable passages and collisions had no correlation (r=0.402). Third, the density of passages and collisions had a very weak positive correlation (r=0.559, p<0.093). Fourth, the use rate of box-type passages did not increase when pipe-type culverts were blocked by water inundation (p=0.561>α=0.05). These results differed from following common expectations: higher numbers and use ratings of passages could cause less frequent collisions, high density areas of passage would cause fewer collisions, and the decreased number of passages would increase the use ratings of remaining passages. Fifth, most monitored mammal species with small-to-medium body sizes used all types of passage structures frequently, but water deer (Hydropotes inermis) rarely used these passage structures of under 0.7 on the openness index. Last, we found by radio telemetry that only one out of 13 radio-collared raccoon dogs was killed by vehicle `collision over a two-year period. However, a total of 12 raccoon dogs that had been killed by cars were found on the same road during the same period.The results of our research can be summarized as follows. First, there were already enough usable passages for wildlife, in spite of seasonal blockage of some passages or the uneven spacing between passages. Second, there were many occurrences of wildlife vehicle collisions, but settlers showed relatively low collision ratio. Third, most collision victims might be wanderers or newcomers unfamiliar to existing passages or occupying settlers. Finally, water deer should be the target species for the construction of wildlife passages, and the size should be O.I of over 0.7. Vehicle collision of other mammal species can be reduced significantly by installing wildlife fences without worsening habitat fragmentation in the case of roads that have many non-wildlife-engineered passages.

  • State Wildlife Action Plans: A resource for State Wildlife Agencies and State Transportation Agencies to Work Together to Prevent Wildlife From Becoming Endangered
    As a requirement of the federal Wildlife Conservation and Restoration Program and State Wildlife Grants program, each state fish and wildlife agency has developed a wildlife action plan, known technically as a "comprehensive wildlife conservation strategy." The wildlife action plans identify the actions that are needed to prevent wildlife from becoming endan¬gered in each state, including habitat conservation, management, restoration, and research and monitoring. Every state has completed an action plan, presenting an historic opportunity to improve the conservation of at-risk wildlife across the nation.Since the wildlife action plans draw together the best scientific data, input from a broad array of experts and stakehold¬ers, and recommendations from prior planning efforts, they present the most comprehensive assessment of what needs to be done in each state to conserve declining and imperiled wildlife. The wildlife action plans complement exist¬ing fish and wildlife management activities focused on recreationally harvested game and sportfish species. Because the action plans are focused on preventing wildlife from becoming endangered, they can be a powerful platform for a range of collaborative, preventive conservation planning and restoration activities.

  • Major Roads: A Filter to the Movement of the Squirrel Glider Petaurus Norfolcensis
    An understanding of the ecological effects of roads and related traffic in highly fragmented landscapes is critical because the viability of wildlife that persist through the adverse impact of habitat loss and fragmentation, due to causes such as agriculture or urban land-uses, may be further impaired by the presence of roads. The potential barrier effect can increase the level of population isolation, especially if traffic volume increases and roads are w3idened. This is particularly the case in landscapes where a large proportion of the habitat occurs in linear strips, such as in hedgerows or along roadsides or watercourses. Much of eastern Australia has been cleared and many threatened species occur in habitat adjacent to roads. Thus, management must minimize the negative effects of roads while maximizing their value for conservation. Gaps in habitat may result in impeded mobility of wildlife and potentially isolate populations, with subsequent consequences for population persistence. The squirrel glider Petaurus norfolcensis can be considered a model species for investigating the impact of roads on connectivity. A native arboreal marsupial, the squirrel glider has a very efficient way of locomotion which consists of gliding between trees, with very rare ventures on the ground, where the risk of predation is higher. Glider movement within home ranges and during dispersal is expected to occur along continuous vegetation, while cleared areas wider than the maximum gliding distance achievable could act as barriers. In this study we evaluated the filter effect of major roads on the squirrel glider in central Victoria (south-eastern Australia) using a combination of radiotracking and genetic techniques. We asked two important questions. First, does a major road act as a barrier or filter to the movement of gliders and if so, does the presence of tall trees between the carriageways facilitate their crossing. A total of 58 adult individuals were radiotracked at six sites along the Hume Freeway (central Victoria), and at two control sites (minor roads with low traffic volume and small or non-existent gap in canopy cover) over a period of six months. The six sites consisted of small roads lined with old growth trees and dissected by the freeway. Three of these sites also had tall trees present in the median section of the freeway. The percentage of animals crossing at sites with vegetated median was similar to that at control sites, with 70% and 79% of all animals observed on the opposite side of the road or the centre median at least once, respectively. In contrast, only one male glider (10% of all animals) was observed crossing at sites with non-vegetated median. Overall, females were less inclined to cross roads, even at control sites and the intensity of crossing was also higher for males than females. The presence of trees in the median of the freeway was thus demonstrated to be a very efficient method of improving connectivity for gliders. Data on dispersal collected via direct methods can be highly informative but also requires intense efforts in field work and usually long term studies. Genetic techniques are a useful alternative to infer dispersal events, through the use of spatial autocorrelation and relatedness/parentage analysis. These methods will be implemented to consolidate the preliminary results and estimate the net effect of observed crossings on gene flow. Mitigation structures consisting of rope bridges and poles are being constructed to improve mobility of gliders as well as a number of other arboreal species and their effectiveness will be monitored using a combination of techniques. These will include motion-detecting infrared cameras, implantable transponders and radiotracking. Data will be compared on a pre- post-mitigation basis and at treatment and control sites.

  • An idiosyncratic perspective on the history and development at the University of California, San Diego of support for cyberinfrastructure-enabled e-science
    A discussion of the history and development of support for cyberinfrastructure and E-Science at the University of California, San Diego.

  • "Why Metadata? Why Me? Why Now?"
    This introductory overview will consider why metadata issues are central to discussions about the evolution of library services--particularly digital library services--and why the cataloging community is, and should be, front and center in those discussions.

  • Vertical Flow Dynamics in Kelp Forests: Implications for Nutrient Uptake, Condition and Survival
    (1) The influence of ocean waves on giant kelp fronds results in the vertical transport of water along the thallus (2) Morphological traits of giant kelp result in vertical transport being greater than in the absence of giant kelp (3) Vertical flow along giant kelp thalli is persistent, but flow rate is correlated with vertical orbital displacements of the incident ocean waves

  • Resources for Teaching Mammalian Neuroanatomy Using Sheep Brains: A Review
    Sheep brain dissection is a mainstay of many neuroscience and biological psychology lab courses. Sheep brain dissection is relatively easy and requires only the brains, surgical gloves, and a large, sharp knife without serrations to provide a valuable learning experience. Preserved sheep brains are readily available from a variety of vendors at a reasonable cost. (Getting brains with the dura already removed is highly recommended because students tend to tear up the brain when removing the dura.) Most structures in the sheep brain are highly homologous to structures in the brains of other placental mammals, including humans. Only cortical structures, particularly sulci and gyri, which are not always homologous across mammalian orders, differ markedly between humans and sheep. Thus, specific facts learned from dissecting sheep brains can be readily generalized to other species. A published hard-copy photographic atlas of the sheep brain is available (Vanderwolf and Cooley, 2002), but searching the internet also reveals many resources made freely available by instructors at a variety of institutions. Most of the websites are designed to be supplements for specific courses, but some are clearly designed for broader use. Many websites could serve as excellent supplements to in-lab dissections, and some could even replace in-lab dissections if resources are tight or if students have ethical objections to using animals.

  • Sex Differences and Organizational Effects of Androgen in Spinal Cord Motor Nuclei
    This article describes a laboratory module taught at UCLA and offers digitized microscope images that will allow instructors to recreate this module at their home institutions with only a computer required. This module allows for 1) an exploration of the effects of hormones on neural development, 2) the demonstration of sex differences in the nervous system, 3) the production of robust and statistically significant data by novice undergraduates, 4) the discussion of sophisticated statistical analyses (ANOVAs with significant main effects and an interaction), and 5) the understanding of at least some of the neuroanatomy of the spinal cord. Specifically, this module both replicates and extends a previously published experiment on sexually dimorphic neurons in the spinal cord of rats (Grisham et al., 1992), which examined the effect of antiandrogen exposure (Flutamide) in utero on sexually dimorphic spinal motoneurons in male and female rats.

  • "Beyond HTML: Developing and re-imagining library web guides in a content management system
    Category: Case Study Purpose: To report on the content management system designed to manage the 30 web-based research guides developed by the subject liaison librarians at the Georgia State University Library. Methodology/Approach: The web development librarian, with assistance from the web programmer, designed a system using MySQL and ASP. A liaison team gave input on the system through rigorous testing and assisted with the design of the templates that control the layout of the content on the guides. A usability study and two surveys were also completed. Findings: The new system met and exceeded the baseline expectations for content collection and management, offering a greater control over appearance and navigation while still offering customization features for liaisons. Improvements are planned for the templates in addition to better promotion of the guides on the library website. Initial and ongoing training for the liaisons should have been more effectively addressed. Despite their observed and future potential advantages, the CMS model has not been universally adopted by academic libraries. Practical Implications: Regardless of the technology involved, libraries preparing for a CMS transition must give at least as much attention to user issues as they do to technical issues, from the organizational buy-in and comprehensive training to internal/external usability. Originality/Value of Paper: This paper contributes to a small but growing collection of CMS case studies. It covers the technical, functional, and managerial developments of a CMS, while also addressing the practical user factors that sometimes get lost in the process. Keywords: content management systems, web-based guides, database-driven websites liaisons, academic libraries

  • Prescribed Fire is Cool on Florida Highway
    Though unprecedented in the sunshine state, plans for a prescribed fire on US319/SR61, Kate Ireland Parkway in north Florida sparked enthusiasm and excitement among roadside managers. The recently expanded high speed corridor passes for ten miles through the Red Hills Region (www.ttrs.org/rhcp); a rural landscape that is host to America's largest remnant of the great longleaf pine forest (www.longleafalliance.org). Prescribed fire is a necessary and popular landscape management tool used by generations of adjoining private land managers with responsibility for conserving this scenic, natural, and cultural resource. Using prescribed fire along this highway is safe and appropriate.It is authorized to maintain a commitment to visually and ecologically restore and reconnect the landscape that is bisected by the four lanes of pavement. Further, the high visibility of this location, provides a dramatic means to inform the public about the benefits of prescribed fire, and to demonstrate that motorists can travel safely in the presence of prescribed fire.Years before the burn, landscape architects, landscape contractors, landscape ecologists, engineers, foresters, firefighters and friends initiated their collaboration with the Florida Department of Transportation and Division of Forestry to prepare a landscape plan and management plan for the corridor. The plan complements the natural beauty and function of the adjoining plantations. Fortunately, Tall Timbers Research Station (www.ttrs.org) is only three miles from the parkway. At Tall Timbers, scientists study the ecology of fire and natural resource management. Without their expertise and leadership, the burn would not have been possible. Finally, after manually and mechanically managing fuels within the wide forested medians, and after planting fire adapted ground cover, understory, and canopy tree species, it was time for the first authorized prescribed burn on a Florida state highway. Weather permitting, the burn was scheduled in concert local news media, and with Florida's annual Prescribed Fire Awareness Week.On schedule, March 7, 2005, from the peach state line, south for one and a half miles, a perfectly executed prescribed burn ignited a new era in Florida roadside management. A traffic control plan similar to what is used during construction, proved safe and effective. Smoke was managed well, except in one instance for a short time near a drain. The Florida Highway Patrol acted quickly to redirect traffic to another lane. There were no accidents or injuries. Eighty percent or more of the targeted median area burned, significantly reducing fuel load and potential for wildfire. Ninety percent or more of the small hardwood sprouts were eliminated, leaving behind the vigorous longleaf pine saplings and clumps of wiregrass. Longleaf saplings were generally scorched back close to the apical meristem, potentially acting as a control on pathogens on the old needles. Cogongrass, Imperata cylindrical, and other invasive plant species known to be in the vicinity thrive after fire. The burn, however, increased their visibility, and provided easier access for treatment. Hundreds of motorists enjoyed a safe driving experience with a close up view of the prescribed burn. Over the following weeks and months thousands enjoyed resprouting foliage and blooming wildflowers.Prescribed burning along the ten miles will continue in three phases, on a three year or shorter interval. In addition to being safe and cost effective, Florida's roadside managers can now report that prescribed burning helps reduce the risk of wildfire, increases native species diversity, enriches habitat, and releases bountiful wildflowers. Though it may never become routine, where appropriate, and where resources and expertise are available, prescribed burning has proven to be safe and effective for roadside vegetation management.

  • Quantifying sediment resuspension linkages to nutrient enrichment in the existing and future Salton Sea
    The UC Davis research involved a 24-month study (including a 4-month measurement program) in the Salton Sea to directly measure sediment resuspension using an array of OBS instruments and an acoustic wave height and current profiling instrument (AWAC). The data provided by these instruments, in conjunction with existing UC Davis temperature recording instruments in the Sea and the existing CIMIS meteorological network, point to the existence of a quasi-equilibrium condition for the suspension of sediments in the lake. Non-linear relations were developed between the wind intensity and turbidity near which were in relative agreement with relationships from reviewed literature. In particular, the extended García and Parker formulation with DLM-WQ shows the best prediction to describe the seasonal trends as well as short-term variations. The relationship was incorporated into the existing DLM-WQ model. DLM-WQ, combined with this new sediment model, was used to more fully explore the potential for ecological restoration of the Salton Sea under possible future configurations. Two scenarios, the North Sea Combined Alternative and South Sea Combined Alternative, as suggested by PEIR were examined. The simulation of North Sea Combined Alternative indicates that the Marine Sea might have a better eutrophic status than that of the whole Sea because of fewer sediment resuspension events due to lower average wind speed acting on a smaller surface. On the other hand, the simulation of South Sea Combined Alternative suggested that the concentrations of nutrients in the water column would be the same or higher than those of the whole Sea, because of more sediment resuspension events due to higher average wind speed and due to shallower water depth. In the both alternatives, however, the anoxia in the hypolimnion would be spatially and temporally increased due to increased stratification periods, during which time toxic substances (such as hydrogen sulfide) and organic materials could be accumulated in the sediments. DLM-WQ with the new sediment algorithm successfully accounts for the dominant processes that control eutrophication in the current Salton Sea and provides an indication of variations in properties that could be expected in potential future configurations. In addition to being a tool for comparing future configurations, DLM-WQ provides a basis for designing future monitoring needs.

  • California-2100: Assessing Future Water Resources over California
    This project implemented the initial phase of California-2100 (Cal21), which is aimed at making and evaluating high resolution estimates of climate change over California out to the year 2100. The initial WRC component of this project has been focused on evaluating how well regional climate models reproduce the variations of important components of the water budget for California, and estimating the effects of the increases over the past century in irrigation in California on regional climate, especially snow accumulation. The results show that global warming has a large effect on precipitation, snow water, surface temperature, low level winds and soil moisture They also show in summer that irrigation has a strong effect on the differences between recent and past conditions in maximum temperature, surface latent and sensible heat fluxes, surface moisture, and surface humidity.

  • Do constructed flow through wetlands improve water quality in the San Joaquin River?
    The efficacy of using constructed wetlands (CW) to improve water quality of irrigation tailwaters was studied in the San Joaquin Valley, California. Two CWs were monitored during the 2004 and 2005 irrigation season, a new CW (W-1) and 12-year-old CW (W-2). Input/output waters from CW were collected weekly and analyzed for a variety of water quality contaminants. Organic carbon, nutrient and sediment retention efficiencies were evaluated from input/output concentrations. Results indicate that CW-2 was more a more efficient contaminant removal system for most water quality constituents. CWs were most effective at removing total suspended solids (TSS). Average TSS removal at CW-2 was 98% in 2004 and 83% in 2005. At CW-1, mean TSS removal was 90% in 2004 and 87% in 2005. Average total N removal efficiency was 41% in 2004 and 29% in 2005 for W-2, compared to 31% in 2004 and 21% in 2005 at W-1. Total P removal efficiency was 63% in 2004 and 24% in 2005 at W-2, compared to 27.5% in 2004 and 11% in 2005 at W-1. Chlorophyll-a, a measure of algal biomass, was higher at W-1, especially in input waters. Initially, in 2004, output concentration of chlorophyll- a increased, however over time, as emergent vegetation established, chlorophyll-a decreased to 35% of input levels. In 2005, CW-2 was a large source of algal biomass because vegetation was not present. Results demonstrate that CWs are effective at capturing sediment and nutrients from irrigation tailwaters, but may be a source of algae if not managed carefully.

  • Non-native fish in mountain lakes: effects on a declining amphibian and ecosystem subsidy
    Wilderness water resources often provide wildlife habitat and associated recreational opportunities, such as angling or birdwatching. Introduced trout in mountain lakes could affect terrestrial wildlife by changing ecosystem subsidy, which is the flow of nutrients and organisms from aquatic to terrestrial habitats. Trout prey upon larval amphibians and aquatic insects, and the adult stages of aquatic insects and amphibians are prey for bats, birds, snakes, and other terrestrial insectivores. The indirect effects of introduced fish on terrestrial wildlife have rarely been considered, and there have been no prior experiments testing effects of fish stocking on the Cascades frog (federal and California species of special concern). We conducted a four-year replicated whole-lake experiment to assess whether changes in fish abundance could aid frog recovery and whether trout predation of larval amphibians and aquatic invertebrates indirectly affects the density of terrestrial predators. Results show that non-native trout suppress the numbers of the declining Cascades frog and other amphibians, as well as large-bodied aquatic insects such as dragonflies and damselflies. After trout removals, these groups show a marked increase in abundance. We found differences in the species and abundance of garter snakes feeding at lakes with and without trout present. Over 100 species of birds and more than six species of bats use the lake basins during the snow-free season and we are currently assessing the data for patterns associated with trout abundances.

  • Development of Biosensors for Real Time Analysis of Perchlorate in Water
    Perchlorate (ClO4 -) contamination of ground water is a widespread problem in the U.S., which can adversely affect human health and wildlife. Current methods for detecting and quantifying ClO4 - in water are time consuming, expensive, and subject to error due to complex procedures and various interferences. Thus, there is an urgent need to develop a method that can accurately detect and measure low concentrations of ClO4 - in the field. This study reports the construction of a ClO4 -- reductase based biosensor for rapid determination of ClO4 - in water. Using a 3 mm GCE (glass carbon electrode), we successfully constructed a ClO4 - sensing bio-electrode by coating an aliquot of the enzyme on nafion (ion-exchange matrix) layer pre-coated on the polished surface of the GCE. Amperometric [i/t] measurements revealed linear increases in current in relation to time and ClO4 - concentration. The biosensor responded strongly to ClO4 - at concentrations as low as 1 μg/L and the sensor displayed a linear response to ClO4 - concentrations in the range 25 to 100 μg/L. Linear response time to ClO4 - at 100 μg/L was approximately111±28 seconds. Kinetic evaluation of the sensor response to ClO4 - revealed linear increases (r2 > 99%) in 10 min with k values of 10.3, 24.2, 33.9 and 48.2 at 25, 50, 75 and 100 μg/L, respectively. A strong linear correlation was established between biosensor response (nA) and ion-chromatography conductivity readings (μS) in the 25 to 100 μg/L linear domain of the biosensor. Biosensor response to ClO4 - was maximal at applied potential range of -0.6 to -1.0V. ClO4 - reduction current increased with an increase in pH and was maximal in the range of 7.6 to 8.0. The ClO4 - biosensor was significantly stable after repeated use (24 analyses conducted on day 1 over a 10-h period at room temperature). This study indicates great potential for the development of a portable biosensor for real time analysis of ClO4 - in water in the field.

  • Structure and seasonal changes of nematode communities from vernal pools (Santa Rosa Plateau)
    Vernal pools are ephemeral wetlands, typically with a diverse and highly adapted flora and fauna. We conducted the first nematode survey on record for this ecologically important habitat. Soil samples were collected on six dates from four locations in and around each of two vernal pool basins in the Santa Rosa Plateau Ecological Reserve. Nematodes from plant roots and debris were extracted in a mist chamber separately from the rest of the soil, which was sieved. An estimated fifty-two nematode genera were isolated, including at least sixty-three species. Soils from the two pools were substantially different in the composition and dynamics of their nematode communities. Nematode abundances were analyzed using the nonparametric Friedman test. Significant differences are observed between/among exact locations, sample dates and extracted sample fractions. Differences in abundance patterns are also significant across nematode genera. Simple feeding experiments were conducted to test whether some vernal pool nematodes might feed on the cysts of fairy shrimp, and thereby potentially limit the recovery of some endangered fairy shrimp species. Our observations do not suggest that this is the case. During the dry summer phase, roots and plant debris appear to play an important role in both pools as refuges for nematodes, and by extension of microscopic organisms in general. Adults of large nematodes, in genera such as Dorylaimus and Labronemella congregate preferentially in dead plant material, perhaps not only in response to drought but also because of the fine texture of the underlying soil. "Aquatic" genera such as Tobrilus persist throughout the dry phase, especially in plant debris. We recommend that management of vernal pools takes care to avoid controlled burns or other forms of removal of dead plant material in dry vernal pool beds. Future surveys of nematodes and other microscopic organisms in this type of alternately inundated and desiccated habitat should include methods for extraction of roots and plant debris.

  • First Scientific Publications from Scripps Institution of Oceanography


  • Consequentialism and Moral Responsibility


  • Watershed Approaches to Compensatory Mitigation: Using Comprehensive Mitigation Planning to Achieve More Mitigation for Transportation Projects
    This research project deals with development of tools and approaches for implementing more effective environmental mitigation for transportation projects. In this presentation we evaluate the availability of tools, methods, and data necessary for implementing comprehensive, watershed-based planning for mitigation for transportation projects, and we present lessons learned from innovative approaches being implemented in the Pacific Northwest. It has long been recognized that project-specific, on-site mitigation projects have high rates of failure, frequently do not achieve the desired environmental benefits, and are very expensive. The emphasis for on-site and in-kind compensatory wetland mitigation makes it difficult to design wetland mitigation projects that are not small, isolated, of limited functional value, and difficult and/or costly to maintain in the long-term. Designing and planning mitigation projects within a watershed or landscape context has long been recognized as necessary for ensuring sustainable, successful mitigation. Transportation projects epitomize these challenges, but also provide some of the best opportunities to create better mitigation alternatives through implementation of watershed approaches. In addition, regulatory agencies are recognizing the importance of watershed approaches. The proposed EPA/COE joint rules for compensatory mitigation explicitly incorporate the need for watershed approaches. How prepared are we, however, to implement watershed approaches in mitigation planning and design? States in the Pacific Northwest have been conducting watershed and basin planning for at least the past 10 years under a number of state and local mandates. This region arguably possesses some of the most complete watershed information available in the United States. To determine the availability of the data necessary for implementing a watershed approach we: (1) evaluated more than 50 watershed and/or basin plans to determine how many plans incorporate key elements of a watershed or landscape approach: spatially explicit, process and function based, both biotic and abiotic processes, multi-species focus; and (2) determined the overlap between locations of transportation projects and watershed data. The majority of watershed plans lack one or more of these key elements. We assess the feasibility of implementing watershed approaches for transportation projects using existing information. Using this analysis, we then discuss the development of innovative tools and databases that are being used for planning for watershed-based mitigation at regional restoration sites. For local, state and federal transportation planning purposes, this allows systematic evaluation of the type and amount of mitigation that is or will be needed in the future for the region or a particular watershed, the existing functional condition of the watershed, and where in the watershed restoration is most needed and will have the greatest benefit.

  • The Salmon Resource and Sensitive Area mapping Project: Integrating a Natural Resource GIS with Field Operations Via Handheld Computer Applications
    The Salmon Resource and Sensitive Area Mapping (SRSAM) project was a unique effort undertaken by the Oregon Department of Transportation (ODOT) to develop a Geographic Information System (GIS) of sensitive natural resource sites integrated with high-resolution digital color infrared imagery for the entire Oregon state highway system (approximately 9,000 miles). SRSAM data allow ODOT to plan maintenance and roadway/bridge project activities with up-to-date environmental resource data by providing maintenance workers, biologists, and transportation planners with access to a current, updateable database of sensitive environmental features.Taking full advantage of the SRSAM GIS for ODOT's transportation planning uses required development of an effective system for delivering information to individual users in the field. To this end, ODOT contracted with Mason, Bruce & Girard, Inc. (MB&G) to develop two handheld computer applications that integrate spatially referenced data, including SRSAM's sensitive resource data, with field data collection forms, thereby allowing users to view, manipulate, and enter data in the field. Use of these applications requires no specialized knowledge of GIS software, empowers users by providing access to an extensive database of environmental information, and through the use of standardized ArcPad forms for routine tasks improves the efficiency of field data collection and management.The first application addresses ODOT's requirements for Mitigation Site Assessment, and enables biologists to spatially identify areas where maintenance or remediation is necessary. This allows a more rapid and efficient response when regulatory performance standards are not being met. The second application focuses on Environmental Scoping, the process by which ODOT identifies environmental issues likely to be associated with proposed projects. This coarse-level assessment requires numerous sources of environmental information. ODOT's Environmental Scoping Application allows users to view over 20 reference data layers, including project-site imagery, while in the field. Other data layers within the Environmental Scoping application are dynamic, allowing users to update and correct spatially referenced environmental information based on their observations. The computer-based forms for both applications obviate the need to transcribe field data collected on paper, thus eliminating a time-consuming and error-prone procedure.Overall, SRSAM has provided a mechanism for ODOT to deliver sensitive natural resource data to maintenance crews, biologists, and transportation planners making field decisions that could impact sensitive resources. ODOT's commitment to completing the SRSAM project state-wide was a key reason that ODOT's routine road maintenance activities received a programmatic exemption under the Federal Endangered Species Act (ESA). The cost to ODOT of not obtaining the programmatic permit for maintenance activities has not been calculated, but surely would have been substantial (millions of dollars). Furthermore, the handheld computer applications, as well as the SRSAM GIS, offer a solution to a difficult ODOT challenge by standardizing data collection and storage techniques throughout the state, thereby streamlining ODOT's efforts to protect sensitive resources. In sum, the SRSAM project represents an innovative,multifaceted solution to ODOT's challenge of environmental compliance and stewardship.

  • A hybrid Gaussian-discrete variable representation approach to molecular continuum processes II: application to photoionization of diatomic Li2+
    We describe an approach for studying molecular photoionization with a hybrid basis that combines the functionality of analytic basis sets to represent electronic coordinates near the nuclei of a molecule with numerically-defined grid-based functions. We discuss the evaluation of the various classes of two-electron integrals that occur in a hybrid basis consisting of Gaussian type orbitals (GTOs) and discrete variable representation (DVR) functions. This combined basis is applied to calculate single photoionization cross sections for molecular Li_2+, which has a large equilibrium bond distance (R=5.86a_0). The highly non-spherical nature of Li_2+ molecules causes higher angular momentum components to contribute significantly to the cross section even at low photoelectron energies, resulting in angular distributions that appear to be f-wave dominated near the photoionization threshold. At higher energies, where the de Broglie wavelength of the photoelectron becomes comparable with the bond distance, interference effects appear in the photoionization cross section. These interference phenomena appear at much lower energies than would be expected for diatomic targets with shorter internuclear separations.

  • Use beam steering dipoles to minimize aberrations associated with off-centered transit through the induction bunching module. Design an improved NDCX-I drift compression section to make best use of the new bunching module to optimize planned initial NDCX-I target experiments
    This milestone has been met by: (1) calculating steering solutions and implementing them in the experiment using the three pairs of crossed magnetic dipoles installed in between the matching solenoids, S1-S4. We have demonstrated the ability to center the beam position and angle to <1 mm and <1 mrad upstream of the induction bunching module (IBM) gap, compared to uncorrected beam offsets of several millimeters and milli-radians. (2) Based on LSP and analytic study, the new IBM, which has twice the volt-seconds of our first IBM, should be accompanied by a longer drift compression section in order to achieve a predicted doubling of the energy deposition on future warm-dense matter targets. This will be accomplished by constructing a longer ferro-electric plasma source. (3) Because the bunched current is a function of the longitudinal phase space and emittance of the beam entering the IBM we have characterized the longitudinal phase space with a high-resolution energy analyzer.

  • Design of Nb3Sn Coils for LARP Long Magnets


  • Preliminary Analysis and Simulation Results of Microwave Transmission Through an Electron Cloud
    The electromagnetic particle-in-cell (PIC) code VORPAL is being used to simulate the interaction of microwave radiation through an electron cloud. The results so far show good agreement with theory for simple cases. The study has been motivated by previous experimental work on this problem at the CERN SPS [1], experiments at the PEP-II Low Energy Ring (LER) at SLAC [4], and proposed experiments at the Fermilab Main Injector (MI). With experimental observation of quantities such as amplitude, phase and spectrum of the output microwave radiation and with support from simulations for different cloud densities and applied magnetic fields, this technique can prove to be a useful probe for assessing the presence as well as the density of electron clouds.

  • Status of the International Muon Ionization Cooling Experiment (MICE)
    An international experiment to demonstrate muon ionization cooling is scheduled for beam at Rutherford Appleton Laboratory (RAL) in 2007. The experiment comprises one cell of the Study II cooling channel [1], along with upstream and downstream detectors to identify individual muons and measure their initial and final 6D phase-space parameters to a precision of 0.1percent. Magnetic design of the beam line and cooling channel are complete and portions are under construction. The experiment will be described, including cooling channel hardware designs, fabrication status, and running plans. Phase 1 of the experiment will prepare the beam line and provide detector systems, including time-of-flight, Cherenkov, scintillating-fiber trackers and their spectrometer solenoids, and an electromagnetic calorimeter. The Phase 2 system will add the cooling channel components, including liquid-hydrogen absorbers embedded in superconducting Focus Coil solenoids, 201-MHz normalconducting RF cavities, and their surrounding Coupling Coil solenoids. The MICE Collaboration goal is to complete the experiment by 2010; progress toward this is discussed.

  • Extracting longitudinal shower development information from crystal calorimetry plus tracking


  • International scoping study: accelerator working group report
    During the past several years, an International Scoping Study (ISS) of a Neutrino Factory was carried out, with the aim of developing an internationally accepted baseline facility design. Progress toward that goal will be described. Many of the key technical aspects of a Neutrino Factory facility design are presently being investigated experimentally, and the status of these investigations will be mentioned. Plans for the recently launched International Design Study (IDS), which serves as a follow-on to the ISS, will be briefly described.

  • Measurements of the asymmetric, dynamic sheath around a pulse biased sphere immersed in flowing metal plasma
    A long-probe technique was utilized to record the expansion and retreat of the dynamic sheath around a spherical substrate immersed in pulsed cathode arc metal plasma. Positively biased, long cylindrical probes were placed on the side and downstream of a negatively pulsed biased stainless steel sphere of 1" (25.4 mm) diameter. The amplitude and width of the negative high voltage pulses (HVP) were 2 kV, 5 kV, 10 kV, and 2 mu s, 4 mu s, 10 mu s, respectively. The variation of the probe (electron) current during the HVP is a direct measure for the sheath expansion and retreat. Maximum sheath sizes were determined for the different parameters of the HVP. The expected rarefaction zone behind the biased sphere (wake) due to the fast plasma flow was clearly established and quantified.

  • Beam energy spread in FERMI@elettra gun and linac induced by intrabeam scattering
    Intrabeam scattering (IBS) of electrons in the pre-cathode area in the electron guns know in the literature as Boersh effect is responsible for a growth of the electron beam energy spread there. Albeit most visible within the electron gun where the electron beam density is large and the energy spread is small, the IBS acts all along the entire electron beam pass through the Linac. In this report we calculate the energy spread induced by IBS in the FERMI@elettra electron gun.

  • The link between a negative high resolution resist contrast/developer performance and the Flory-Huggins parameter estimated from the Hansen solubility sphere


  • Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus
    Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolates from diverse areas of the world's oceans have been studied and shown to be physiologically and genetically distinct. All isolates described thus far can be assigned to either a tightly clustered high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted group. The 16S rRNA sequences of the entire Prochlorococcus group differ by at most 3percent, and the four initially published genomes revealed patterns of genetic differentiation that help explain physiological differences among the isolates. Here we describe the genomes of eight newly sequenced isolates and combine them with the first four genomes for a comprehensive analysis of the core (shared by all isolates) and flexible genes of the Prochlorococcus group, and the patterns of loss and gain of the flexible genes over the course of evolution. There are 1,273 genes that represent the core shared by all 12 genomes. They are apparently sufficient, according to metabolic reconstruction, to encode a functional cell. We describe a phylogeny for all 12 isolates by subjecting their complete proteomes to three different phylogenetic analyses. For each non-core gene, we used a maximum parsimony method to estimate which ancestor likely first acquired or lost each gene. Many of the genetic differences among isolates, especially for genes involved in outer membrane synthesis and nutrient transport, are found within the same clade. Nevertheless, we identified some genes defining HL and LL ecotypes, and clades within these broad ecotypes, helping to demonstrate the basis of HL and LL adaptations in Prochlorococcus. Furthermore, our estimates of gene gain events allow us to identify highly variable genomic islands that are not apparent through simple pairwise comparisons. These results emphasize the functional roles, especially those connected to outer membrane synthesis and transport that dominate the flexible genome and set it apart from the core. Besides identifying islands and demonstrating their role throughout the history of Prochlorococcus, reconstruction of past gene gains and losses shows that much of the variability exists at the "leaves of the tree," between the most closely related strains. Finally, the identification of core and flexible genes from this 12-genome comparison is largely consistent with the relative frequency of Prochlorococcus genes found in global ocean metagenomic databases, further closing the gap between our understanding of these organisms in the lab and the wild.

  • A Korarchael Genome Reveals Insights into the Evolution of the Archaea
    The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota. Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, ?Candidatus Korarchaeum cryptofilum,? which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49percent. Of the 1,617 predicted protein-coding genes, 1,382 (85percent) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota. However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota. In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.

  • Volumetric strains of clean sands subject to cyclic loads
    We utilize simple shear testing to investigate the volume change of clean sands subject to cyclic loads. We examine the effects of a number of compositional and environmental factors on the vertical strain at 15 uniform shear strain cycles and on the cycle-to-cycle variation of vertical strain. The compositional factor found to principally affect seismic compression susceptibility is relative density (DR). Compositional factors found to not significantly affect cyclic volume change include gradation parameters (mean grain size, uniformity coefficient), particle angularity, soil fabric, mineralogy, and void ratio "breadth" e-emin. An environmental factor found to affect seismic compression susceptibility is confining stress, with volumetric strains decreasing with increasing stress. Environmental factors that do not significantly affect seismic compression susceptibility for clean sands are saturation and age. Stress history can decrease vertical strains from seismic compression for certain conditions, but we find such effects to not be significant for the levels of overburden stress where compacted fills are typically overconsolidated from compaction-induced stresses. An empirical model is developed to represent the major trends of the data for application in engineering practice, which improves upon an earlier model that is based on a much smaller database and which does not account for the aforementioned environmental factors.

  • Washington State Department of Transportation Bridge Maintenance and Inspection Guidance for Protected Terrestrial Species
    Protected wildlife species that utilize the Washington State Department of Transportation (WSDOT) bridges and structures may be susceptible to impacts from routine maintenance and inspection activities. In response to community-driven concerns related to the conservation of protected terrestrial species and due to the lack of existing guidance for bridge related activities, WSDOT expanded their Highway Maintenance Environmental Compliance Guidance for Protected Terrestrial Species to include guidance for bridges. Two documents were developed, one document specific to bridge inspection activities, and one specific to maintenance activities. The guidance is performance outcome based, and requires that inspection and maintenance activities avoid adverse impacts to nesting protected birds and other wildlife. The guidance has been implemented and is successfully being used by bridge inspection and maintenance staff.

  • Sonoran Desert Conservation Plan and Regional Transportation Planning: A Case Study in Challenges for Protecting and Restoring Wildlife Connectivity in Urbanized Areas
    This project demonstrates full integration of habitat conservation, transportation, and land use planning on a local and multi-jurisdictional level, utilizing best available science and best practices.The Coalition for Sonoran Desert Protection, an alliance of 38 conservation and community groups, formed in 1998 to protect biodiversity in the Sonoran Desert through Pima County's multi-species habitat conservation planning effort. Pima County, encompassing over 9 million acres of metropolitan Tucson, Arizona and vast rural landscapes, is adjacent to the Mexican border state of Sonora, Mexico. The metropolitan Tucson area is the focus of the planning area, whose population is expected to reach 1 million by the end of 2006. Encompassing Tucson on four sides is federal forest and park lands. The planning process brought together scientists from state and federal agencies, advocates from NGO's, and local county and municipal officials. A broad group of stakeholders was also convened to produce consensus recommenda¬tions to county officials regarding ESA Section 10 compliance. This abstract will outline the steps taken to protect and re-create wildlife linkages utilizing transportation projects through local planning and cooperative creative partner¬ships.Methodology in the broad context of protecting biodiversity included a 4-year development, by a science technical team, of a county-wide map identifying and prioritizing biologically-important lands. Categories developed were: Important Riparian Areas, Biological Core Management Areas, Special Species Management Areas, Multiple-Use Management Areas, and Critical Landscape Linkages. As connectivity between reserves was of particular importance to a functional landscape, the linkages category became a focus with its own methodology for implementation.Critical Landscape Linkages have been defined as, areas that contain potential connectivity corridors for biological resources but also may have now, or in the future, barriers that tend to isolate major conservation areas. The linkage definitions, maps, and land use guidelines have been included in both the draft habitat conservation plan and the county's comprehensive land use plan. The barriers consist of highways, roads, and a federal irrigation (Colorado River) canal. Methodology to design, implement and construct wildlife connectivity through transportation barriers has been multi-faceted and complex. The Coalition was able to bring attention to the importance of the issue to local officials, adopt the linkages in local public documents, successfully advocate for the adoption of environmentally-sensitive roadway design guidelines, successfully pass voter-approved Open Space Bonds of $174.3 million which includes acquisition of lands within mapped linkages adjacent to roads, and education and cooperation of other road-building agencies. As well, the Coalition Director was involved with state legislation that created a county-wide Regional Transportation Authority to which she was appointed. Through that committee, the Coalition was able to successfully advocate for adoption of a program category for Critical Landscape Linkages that includes $45 million to be expended for wildlife structures. This plan and funding was adopted by county voters in May 2006 as part of a 20-year, $2.1 billion trans¬portation package.Both the 2004 Open Space Bond acquisitions and the Critical Landscape Linkages funding for wildlife crossing structures are currently being implemented. These programs are being integrated not only with each other, but with multi-jurisdictional land use planning decisions, and on-going research and monitoring.There is a huge opportunity in future research, which needs to include intensive monitoring of the linkages and their contribution to protection and restoring biodiversity in the Sonoran Desert.Although this process, begun in 1998, was a direct response to endangered species liability issues county-wide, the scientific and community response has gone far beyond the regulatory compliance. If accepted, the paper will outline in greater detail the technical and biological issues involved in the local process, with particular focus on the chal¬lenges faced in successful integration of transportation and conservation planning.

  • Application of Ecological Assessments to Regional and Statewide Transportation Planning
    The application of ecological assessments can facilitate transportation project planning and delivery that can avoid or minimize impacts to the environment and minimize disruptions of critical ecological processes. This presentation considers the value of ecological assessments designed to integrate regional conservation planning with environmental regulatory compliance that support ecologically appropriate transportation planning and project delivery. Recent transportation legislation (SAFETEA-LU) requires transportation agencies to consider environmental considerations in their regional and state-wide transportation plans, Earlier transportation required Federal agencies to coordinate environmental reviews to address multiple regulatory compliance simultaneously rather sequentially whenever possible. This requirement has been retained in the in SAFETEA-LU. Ecological assessments have been developed to address a variety of objectives. This presentation will review a subset of assessments and discuss components of those assessments which may offer the greatest value to transportation planners. This presentation will offer a template for developing a rapid assessment that offer a menu of assessment components that state and local transportation planners may consider to facilitate compliance with the new planning regulations that result in streamlined planning and project delivery. After the passage of SAFETEA-LU, the national Academy of Sciences hosted a workshop to discuss the information needs necessary to support the new provisions such as these new environmental within the recent legislation. The presentation will offer a list of date needs that facilitate the coordination and integration of multiple agency considerations and regulatory requirements. Follow-up work could include and analysis of the rapid assessment process and how it can be continually improved.

  • Spatial analysis of marine turtle strandings data in the Hawaiian Islands for the period 2002-2007
    Geographic Information Systems (GIS) is becoming a very important and useful tool in conservation planning and is applied here to examine the relationship between marine turtles and their environment in the Hawaiian Islands. This project spatially analyzed the locations of marine turtle strandings reported in Hawaii over a six-year period (2002 - 2007). The data include location, assigned cause of stranding, and other related characteristics relevant to the strandings such as presence of Fibropapillomatosis (FP, a tumor-forming disease) and evidence of fishing gear interaction. The use of spatial analysis for both coastal fishing gear interactions and hawksbill turtle strandings was useful for a visual representation of these events; however, no significant patterns were discovered. The spatial analysis of the stranding data in combination with environmental parameters proved most interesting. Overall, there is a strong correlation between FP-related strandings and areas of limited water quality and human population, respectively, and a moderate correlation between FP-related strandings and agricultural lands. A high prevalence of FP has been shown in previous studies to correspond to coastal waters characterized by habitat degradation and pollution, suggesting that one or more of these factors could serve as an environmental cofactor in the development of FP. A clear target for mitigation strategies that would benefit not only marine turtles afflicted with this disease, but all other organisms that share the same ecosystem, is water quality improvement in coastal areas of the Hawaiian Islands.

  • "Mill's Extraordinary Utilitarian Moral Theory"


  • "Philosophical Lessons from Positive Psychology"


  • "Mill's Conception of Human Rights"


  • "The Utilitarian Influence on American Legal Science in the Early Republic"


  • "Utilitarian Political Economy, Natural Rights and the Poor"


  • Allen: Winfred Emory Allen Biography


  • Nierenberg: William Aaron Nierenberg Biography


  • Sargent: Marson Cleaves Sargent and Grace 'Peter' Charlotte Tompkins Sargent Biographies


  • Dietz: Robert Sinclair Dietz Biography