Showing papers by "University of California, Santa Barbara published in 2002"

Initial sequencing and comparative analysis of the mouse genome.

Abstract: The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

Chaotic Mixer for Microchannels

Abstract: It is difficult to mix solutions in microchannels. Under typical operating conditions, flows in these channels are laminar—the spontaneous fluctuations of velocity that tend to homogenize fluids in turbulent flows are absent, and molecular diffusion across the channels is slow. We present a passive method for mixing streams of steady pressure-driven flows in microchannels at low Reynolds number. Using this method, the length of the channel required for mixing grows only logarithmically with the Pe «clet number, and hydrodynamic dispersion along the channel is reduced relative to that in a simple, smooth channel. This method uses bas-relief structures on the floor of the channel that are easily fabricated with commonly used methods of planar lithography.

Critical Race Methodology: Counter-Storytelling as an Analytical Framework for Education Research:

Abstract: This article addresses how critical race theory can inform a critical race methodology in education. The authors challenge the intercentricity of racism with other forms of subordination and exposes deficit-informed research that silences and distorts epistemologies of people of color. Although social scientists tell stories under the guise of “objective” research, these stories actually uphold deficit, racialized notions about people of color. For the authors, a critical race methodology provides a tool to “counter” deficit storytelling. Specifically, a critical race methodology offers space to conduct and present research grounded in the experiences and knowledge of people of color. As they describe how they compose counter-stories, the authors discuss how the stories can be used as theoretical, methodological, and pedagogical tools to challenge racism, sexism, and classism and work toward social justice.

Understanding Social Preferences with Simple Tests

Abstract: Departures from self-interest in economic experiments have recently inspired models of “social preferences” We design a range of simple experimental games that test these theories more directly than existing experiments Our experiments show that subjects are more concerned with increasing social welfare—sacrificing to increase the payoffs for all recipients, especially low-payoff recipients—than with reducing differences in payoffs (as supposed in recent models) Subjects are also motivated by reciprocity: They withdraw willingness to sacrifice to achieve a fair outcome when others are themselves unwilling to sacrifice, and sometimes punish unfair behavior

Hierarchies from fluxes in string compactifications

Abstract: Warped compactifications with significant warping provide one of the few known mechanisms for naturally generating large hierarchies of physical scales. We demonstrate that this mechanism is realizable in string theory, and give examples involving orientifold compactifications of type-IIB string theory and F-theory compactifications on Calabi-Yau fourfolds. In each case, the hierarchy of scales is fixed by a choice of Ramond-Ramond and Neveu-Schwarz fluxes in the compact manifold. Our solutions involve compactifications of the Klebanov-Strassler gravity dual to a confining $\mathcal{N}=1$ supersymmetric gauge theory, and the hierarchy reflects the small scale of chiral symmetry breaking in the dual gauge theory.

Abscisic Acid Signaling in Seeds and Seedlings

Abstract: Abscisic acid (ABA) regulates many agronomically important aspects of plant development, including the synthesis of seed storage proteins and lipids, the promotion of seed desiccation tolerance and dormancy, and the inhibition of the phase transitions from embryonic to germinative growth and from

AlGaN/GaN HEMTs-an overview of device operation and applications

Abstract: Wide bandgap semiconductors are extremely attractive for the gamut of power electronics applications from power conditioning to microwave transmitters for communications and radar. Of the various materials and device technologies, the AlGaN/GaN high-electron mobility transistor seems the most promising. This paper attempts to present the status of the technology and the market with a view of highlighting both the progress and the remaining problems.

The Holographic principle

Abstract: There is strong evidence that the area of any surface limits the information content of adjacent spacetime regions, at $1.4\ifmmode\times\else\texttimes\fi{}{10}^{69}$ bits per square meter. This article reviews the developments that have led to the recognition of this entropy bound, placing special emphasis on the quantum properties of black holes. The construction of light sheets, which associate relevant spacetime regions to any given surface, is discussed in detail. This article explains how the bound is tested, and its validity is demonstrated in a wide range of examples. A universal relation between geometry and information is thus uncovered. It has yet to be explained. The holographic principle asserts that its origin must lie in the number of fundamental degrees of freedom involved in a unified description of spacetime and matter. It must be manifest in an underlying quantum theory of gravity. This article surveys some successes and challenges in implementing the holographic principle.

A secure routing protocol for ad hoc networks

Abstract: Most recent ad hoc network research has focused on providing routing services without considering security. We detail security threats against ad hoc routing protocols, specifically examining AODV and DSR. In light of these threats, we identify three different environments with distinct security requirements. We propose a solution to one, the managed-open scenario where no network infrastructure is pre-deployed, but a small amount of prior security coordination is expected. Our protocol, authenticated routing for ad hoc networks (ARAN), is based on certificates and successfully defeats all identified attacks.

e-Learning and the Science of Instruction: Proven Guidelines for Consumers and Designers of Multimedia Learning

Abstract: In this thoroughly revised edition of the bestselling e-Learning and the Science of Instruction authors Ruth Colvin Clark and Richard E. Mayer internationally-recognized experts in the field of e-learningoffer essential information and guidelines for selecting, designing, and developing asynchronous and synchronous e-learning courses that build knowledge and skills for workers learning in corporate, government, and academic settings. In addition to updating research in all chapters, two new chapters and a CD with multimedia examples are included.

The Cambridge Introduction to Narrative

Abstract: What is narrative? How does it work and how does it shape our lives? H. Porter Abbott emphasizes that narrative is found not just in literature, film, and theatre, but everywhere in the ordinary course of people's lives. This widely used introduction, now revised and expanded in its third edition, is informed throughout by recent developments in the field and includes one new chapter. The glossary and bibliography have been expanded, and new sections explore unnatural narrative, retrograde narrative, reader-resistant narratives, intermedial narrative, narrativity, and multiple interpretation. With its lucid exposition of concepts, and suggestions for further reading, this book is not only an excellent introduction for courses focused on narrative but also an invaluable resource for students and scholars across a wide range of fields, including literature and drama, film and media, society and politics, journalism, autobiography, history, and still others throughout the arts, humanities, and social sciences.

2001 Consensus Guidelines for the Management of Women With Cervical Cytological Abnormalities

Abstract: ObjectiveTo provide evidence-based consensus guidelines for the management of women with cervical cytological abnormalities and cervical cancer precursors.ParticipantsA panel of 121 experts in the diagnosis and management of cervical cancer precursors, including representatives from 29 professional organizations, federal agencies, and national and international health organizations, were invited to participate in a consensus conference sponsored by the American Society for Colposcopy and Cervical Pathology (ASCCP).Evidence and Consensus ProcessGuidelines for the management of women with cervical cytological abnormalities were developed through a multistep process. Starting 6 months before the conference, working groups developed draft management guidelines based on formal literature reviews of English-language articles published in 1988-2001, as well as input from the professional community at large, obtained using interactive Internet-based bulletin boards. On September 6-8, 2001, the ASCCP Consensus Conference was held in Bethesda, Md. Guidelines with supporting evidence were presented and underwent discussion, revision, and voting.ConclusionsManagement of women with atypical squamous cells (ASC) depends on whether the Papanicolaou test is subcategorized as of undetermined significance (ASC-US) or as cannot exclude high-grade squamous intraepithelial lesion (HSIL) (ASC-H). Women with ASC-US should be managed using a program of 2 repeat cytology tests, immediate colposcopy, or DNA testing for high-risk types of human papillomavirus (HPV). Testing for HPV DNA is the preferred approach when liquid-based cytology is used for screening. In most instances, women with ASC-H, low-grade squamous intraepithelial lesion, HSIL, and atypical glandular cells should be referred for immediate colposcopic evaluation.

Rainfall variability, carbon cycling, and plant species diversity in a mesic grassland

Abstract: Ecosystem responses to increased variability in rainfall, a prediction of general circulation models, were assessed in native grassland by reducing storm frequency and increasing rainfall quantity per storm during a 4-year experiment. More extreme rainfall patterns, without concurrent changes in total rainfall quantity, increased temporal variability in soil moisture and plant species diversity. However, carbon cycling processes such as soil CO2 flux, CO2 uptake by the dominant grasses, and aboveground net primary productivity (ANPP) were reduced, and ANPP was more responsive to soil moisture variability than to mean soil water content. Our results show that projected increases in rainfall variability can rapidly alter key carbon cycling processes and plant community composition, independent of changes in total precipitation.

SAR11 clade dominates ocean surface bacterioplankton communities

Abstract: The most abundant class of bacterial ribosomal RNA genes detected in seawater DNA by gene cloning belongs to SAR11-an alpha-proteobacterial clade. Other than indications of their prevalence in seawater, little is known about these organisms. Here we report quantitative measurements of the cellular abundance of the SAR11 clade in northwestern Sargasso Sea waters to 3,000 m and in Oregon coastal surface waters. On average, the SAR11 clade accounts for a third of the cells present in surface waters and nearly a fifth of the cells present in the mesopelagic zone. In some regions, members of the SAR11 clade represent as much as 50% of the total surface microbial community and 25% of the subeuphotic microbial community. By extrapolation, we estimate that globally there are 2.4 x 10(28) SAR11 cells in the oceans, half of which are located in the euphotic zone. Although the biogeochemical role of the SAR11 clade remains uncertain, these data support the conclusion that this microbial group is among the most successful organisms on Earth.

Outgassing from Amazonian rivers and wetlands as a large tropical source of atmospheric CO2.

Abstract: Terrestrial ecosystems in the humid tropics play a potentially important but presently ambiguous role in the global carbon cycle. Whereas global estimates of atmospheric CO2 exchange indicate that the tropics are near equilibrium or are a source with respect to carbon, ground-based estimates indicate that the amount of carbon that is being absorbed by mature rainforests is similar to or greater than that being released by tropical deforestation (about 1.6 Gt C yr-1). Estimates of the magnitude of carbon sequestration are uncertain, however, depending on whether they are derived from measurements of gas fluxes above forests or of biomass accumulation in vegetation and soils. It is also possible that methodological errors may overestimate rates of carbon uptake or that other loss processes have yet to be identified. Here we demonstrate that outgassing (evasion) of CO2 from rivers and wetlands of the central Amazon basin constitutes an important carbon loss process, equal to 1.2 +/- 0.3 Mg C ha-1 yr-1. This carbon probably originates from organic matter transported from upland and flooded forests, which is then respired and outgassed downstream. Extrapolated across the entire basin, this flux-at 0.5 Gt C yr-1-is an order of magnitude greater than fluvial export of organic carbon to the ocean. From these findings, we suggest that the overall carbon budget of rainforests, summed across terrestrial and aquatic environments, appears closer to being in balance than would be inferred from studies of uplands alone.

Positive Behavior Support: Evolution of an Applied Science

Abstract: Positive behavior support (PBS) is an applied science that uses educational and systems change methods (environmental redesign) to enhance quality of life and minimize problem behavior. PBS initial...

High-energy colliders as black hole factories: The End of short distance physics

Abstract: If the fundamental Planck scale is of order of a TeV, as is the case in some extra-dimension scenarios, future hadron colliders such as the CERN Large Hadron Collider will be black hole factories. The nonperturbative process of black hole formation and decay by Hawking evaporation gives rise to spectacular events with up to many dozens of relatively hard jets and leptons with a characteristic ratio of hadronic to leptonic activity of roughly 5:1. The total transverse energy of such events is typically a sizable fraction of the beam energy. Perturbative hard scattering processes at energies well above the Planck scale are cloaked behind a horizon, thus limiting the ability to probe short distances. The high energy black hole cross section grows with energy at a rate determined by the dimensionality and geometry of the extra dimensions. This dependence therefore probes the extra dimensions at distances larger than the Planck scale.

Effects of drying–rewetting frequency on soil carbon and nitrogen transformations

Abstract: Soil drying and rewetting impose a significant stress on the soil microbial community. While wetting events are common in most environments, the short and long-term effects of soil rewetting on microbial processes have not been well studied. Furthermore, it is not clear if stress history is important to consider when modeling microbial controls on ecosystem dynamics. In this experiment, we manipulated the frequency of soil rewetting events during 2 months to determine how stress history influences the response of soil microbial communities to rewetting events. Two soils were collected from the Sedgwick Ranch Natural Reserve in Santa Ynez, CA, one from an annual grassland, the other from underneath an oak canopy. Soils were incubated in the lab and went through either 0, 1, 2, 4, 6, 9, or 15 drying–rewetting cycles over 2 months. Soil moisture content was adjusted so that the average moisture content over the course of the incubation was the same for all samples, compensating for the number of drying–rewetting cycles. Soils were analyzed for respiration rate, substrate utilization efficiency, nitrification potential, microbial biomass, and NH4+ and NO3− concentrations. Total CO2 loss during incubation significantly increased with number of rewetting events for oak soils but not for grass soils, where a large number of rewetting events decreased total CO2 loss. Exposure to frequent drying–rewetting events decreased the amount of CO2 released upon rewetting and dramatically increased the activity of autotrophic nitrifier populations. For up to 6 weeks after the last drying–rewetting cycle, respiration rates in soils exposed to a history of drying–rewetting events were substantially lower than their non-stressed controls. In all cases, the effects of the rewetting stress were greater in oak than in grass soils. The results indicate that drying–rewetting events can induce significant changes in microbial C and N dynamics and these effects can last for more than a month after the last stress. The frequency of drying–rewetting stress events has important ecosystem-level ramifications and should be incorporated into models of soil microbial dynamics.

Comparison of Riemann and Lebesgue sampling for first order stochastic systems

Abstract: The normal approach to digital control is to sample periodically in time. Using an analog of integration theory we can call this Riemann sampling. Lebesgue sampling or event based sampling is an alternative to Riemann sampling. It means that signals are sampled only when measurements pass certain limits. In this paper it is shown that Lebesgue sampling gives better performance for some simple systems.

A measurement by BOOMERANG of multiple peaks in the angular power spectrum of the cosmic microwave background

Abstract: This paper presents a measurement of the angular power spectrum of the cosmic microwave background from l = 75 to l = 1025 (~10' to 24) from a combined analysis of four 150 GHz channels in the BOOMERANG experiment. The spectrum contains multiple peaks and minima, as predicted by standard adiabatic inflationary models in which the primordial plasma undergoes acoustic oscillations. These results, in concert with other types of cosmological measurements and theoretical models, significantly constrain the values of ?tot, ?bh2, ?ch2, and ns.

Distributed control of spatially invariant systems

Abstract: We consider distributed parameter systems where the underlying dynamics are spatially invariant, and where the controls and measurements are spatially distributed. These systems arise in many applications such as the control of vehicular platoons, flow control, microelectromechanical systems (MEMS), smart structures, and systems described by partial differential equations with constant coefficients and distributed controls and measurements. For fully actuated distributed control problems involving quadratic criteria such as linear quadratic regulator (LQR), H/sub 2/ and H/sub /spl infin//, optimal controllers can be obtained by solving a parameterized family of standard finite-dimensional problems. We show that optimal controllers have an inherent degree of decentralization, and this provides a practical distributed controller architecture. We also prove a general result that applies to partially distributed control and a variety of performance criteria, stating that optimal controllers inherit the spatial invariance structure of the plant. Connections of this work to that on systems over rings, and systems with dynamical symmetries are discussed.

A cross-ecosystem comparison of the strength of trophic cascades

Abstract: Although trophic cascades (indirect effects of predators on plants via herbivores) occur in a wide variety of food webs, the magnitudes of their effects are often quite variable. We compared the responses of herbivore and plant communities to predator manipulations in 102 field experiments in six different ecosystems: lentic ( lake and pond), marine, and stream benthos, lentic and marine plankton, and terrestrial (grasslands and agricultural fields). Predator effects varied considerably among systems and were strongest in lentic and marine benthos and weakest in marine plankton and terrestrial food webs. Predator effects on herbivores were generally larger and more variable than on plants, suggesting that cascades often become attenuated at the plant‐ herbivore interface. Top-down control of plant biomass was stronger in water than on land; however, the differences among the five aquatic food webs were as great as those between wet and dry systems.

Optimization of a semianalytical ocean color model for global-scale applications

Abstract: Semianalytical (SA) ocean color models have advantages over conventional band ratio algorithms in that multiple ocean properties can be retrieved simultaneously from a single water-leaving radiance spectrum. However, the complexity of SA models has stalled their development, and operational implementation as optimal SA parameter values are hard to determine because of limitations in development data sets and the lack of robust tuning procedures. We present a procedure for optimizing SA ocean color models for global applications. The SA model to be optimized retrieves simultaneous estimates for chlorophyll (Chl) concentration, the absorption coefficient for dissolved and detrital materials [a(cdm)(443)], and the particulate backscatter coefficient [b(bp)(443)] from measurements of the normalized water-leaving radiance spectrum. Parameters for the model are tuned by simulated annealing as the global optimization protocol. We first evaluate the robustness of the tuning method using synthetic data sets, and we then apply the tuning procedure to an in situ data set. With the tuned SA parameters, the accuracy of retrievals found with the globally optimized model (the Garver-Siegel-Maritorena model version 1; hereafter GSM01) is excellent and results are comparable with the current Sea-viewing Wide Field-of-view sensor (SeaWiFS) algorithm for Chl. The advantage of the GSM01 model is that simultaneous retrievals of a(cdm)(443) and b(bp)(443) are made that greatly extend the nature of global applications that can be explored. Current limitations and further developments of the model are discussed.

PatternHunter: faster and more sensitive homology search

Abstract: Motivation: Genomics and proteomics studies routinely depend on homology searches based on the strategy of finding short seed matches which are then extended. The exploding genomic data growth presents a dilemma for DNA homology search techniques: increasing seed size decreases sensitivity whereas decreasing seed size slows down computation. Results: We present a new homology search algorithm ‘PatternHunter’ that uses a novel seed model for increased sensitivity and new hit-processing techniques for significantly increased speed. At Blast levels of sensitivity, PatternHunter is able to find homologies between sequences as large as human chromosomes, in mere hours on a desktop. Availability: PatternHunter is available at http://www. bioinformaticssolutions.com, as a commercial package. It runs on all platforms that support Java. PatternHunter technology is being patented; commercial use requires a license from BSI, while non-commercial use will be free.

Hard scattering and gauge/string duality.

Abstract: We consider high-energy fixed-angle scattering of glueballs in confining gauge theories that have supergravity duals. Although the effective description is in terms of the scattering of strings, we find that the amplitudes are hard (power law). This is a consequence of the warped geometry of the dual theory, which has the effect that in an inertial frame the string process is never in the soft regime. At small angle we find hard and Regge behaviors in different kinematic regions.

The BABAR detector

Abstract: BABAR, the detector for the SLAC PEP-II asymmetric e+e- B Factory operating at the upsilon 4S resonance, was designed to allow comprehensive studies of CP-violation in B-meson decays. Charged particle tracks are measured in a multi-layer silicon vertex tracker surrounded by a cylindrical wire drift chamber. Electromagentic showers from electrons and photons are detected in an array of CsI crystals located just inside the solenoidal coil of a superconducting magnet. Muons and neutral hadrons are identified by arrays of resistive plate chambers inserted into gaps in the steel flux return of the magnet. Charged hadrons are identified by dE/dx measurements in the tracking detectors and in a ring-imaging Cherenkov detector surrounding the drift chamber. The trigger, data acquisition and data-monitoring systems, VME- and network-based, are controlled by custom-designed online software. Details of the layout and performance of the detector components and their associated electronics and software are presented.

Rapidly recovering hydrogel scaffolds from self-assembling diblock copolypeptide amphiphiles

Abstract: Protein-based hydrogels are used for many applications, ranging from food and cosmetic thickeners to support matrices for drug delivery and tissue replacement. These materials are usually prepared using proteins extracted from natural sources, which can give rise to inconsistent properties unsuitable for medical applications. Recent developments have utilized recombinant DNA methods to prepare artificial protein hydrogels with specific association mechanisms and responsiveness to various stimuli. Here we synthesize diblock copolypeptide amphiphiles containing charged and hydrophobic segments. Dilute solutions of these copolypeptides would be expected to form micelles; instead, they form hydrogels that retain their mechanical strength up to temperatures of about 90 degrees C and recover rapidly after stress. The use of synthetic materials permits adjustment of copolymer chain length and composition, which we varied to study their effect on hydrogel formation and properties. We find that gelation depends not only on the amphiphilic nature of the polypeptides, but also on chain conformations--alpha-helix, beta-strand or random coil. Indeed, shape-specific supramolecular assembly is integral to the gelation process, and provides a new class of peptide-based hydrogels with potential for applications in biotechnology.