Showing papers by "University of California published in 1999"

Blobworld: A System for Region-Based Image Indexing and Retrieval

Abstract: Blobworld is a system for image retrieval based on finding coherent image regions which roughly correspond to objects. Each image is automatically segmented into regions ("blobs") with associated color and texture descriptors. Queryingi s based on the attributes of one or two regions of interest, rather than a description of the entire image. In order to make large-scale retrieval feasible, we index the blob descriptions usinga tree. Because indexing in the high-dimensional feature space is computationally prohibitive, we use a lower-rank approximation to the high-dimensional distance. Experiments show encouraging results for both queryinga nd indexing.

Picosecond–milliångström lattice dynamics measured by ultrafast X-ray diffraction

Abstract: Fundamental processes on the molecular level, such as vibrations and rotations in single molecules, liquids or crystal lattices and the breaking and formation of chemical bonds, occur on timescales of femtoseconds to picoseconds. The electronic changes associated with such processes can be monitored in a time-resolved manner by ultrafast optical spectroscopic techniques1, but the accompanying structural rearrangements have proved more difficult to observe. Time-resolved X-ray diffraction has the potential to probe fast, atomic-scale motions2,3,4,5. This is made possible by the generation of ultrashort X-ray pulses6,7,8,9,10, and several X-ray studies of fast dynamics have been reported6,7,8,11,12,13,14,15. Here we report the direct observation of coherent acoustic phonon propagation in crystalline gallium arsenide using a non-thermal, ultrafast-laser-driven plasma — a high-brightness, laboratory-scale source of subpicosecond X-ray pulses16,17,18,19. We are able to follow a 100-ps coherent acoustic pulse, generated through optical excitation of the crystal surface, as it propagates through the X-ray penetration depth. The time-resolved diffraction data are in excellent agreement with theoretical predictions for coherent phonon excitation20 in solids, demonstrating that it is possible to obtain quantitative information on atomic motions in bulk media during picosecond-scale lattice dynamics.

A hybrid user model for news story classification

Abstract: We present an intelligent agent designed to compile a daily news program for individual users. Based on feedback from the user, the system automatically adapts to the user’s preferences and interests. In this paper we focus on the system’s user modeling component. First, we motivate the use of a multi-strategy machine learning approach that allows for the induction of user models that consist of separate models for long-term and short-term interests. Second, we investigate the utility of explicitly modeling information that the system has already presented to the user. This allows us to address an important issue that has thus far received virtually no attention in the Information Retrieval community: the fact that a user’s information need changes as a direct result of interaction with information. We evaluate the proposed algorithms on user data collected with a prototype of our system, and assess the individual performance contributions of both model components.

UMAC: Fast and Secure Message Authentication

Abstract: We describe a message authentication algorithm, UMAC, which can authenticate messages (in software, on contemporary machines) roughly an order of magnitude faster than current practice (e.g., HMAC-SHA1), and about twice as fast as times previously reported for the universal hash-function family MMH. To achieve such speeds, UMAC uses a new universal hash-function family, NH, and a design which allows effective exploitation of SIMD parallelism. The "cryptographic" work of UMAC is done using standard primitives of the user's choice, such as a block cipher or cryptographic hash function; no new heuristic primitives are developed here. Instead, the security of UMAC is rigorously proven, in the sense of giving exact and quantitatively strong results which demonstrate an inability to forge UMAC-authenticated messages assuming an inability to break the underlying cryptographic primitive. Unlike conventional, inherently serial MACs, UMAC is parallelizable, and will have ever-faster implementation speeds as machines offer up increasing amounts of parallelism. We envision UMAC as a practical algorithm for next-generation message authentication.

Elements of Good Route Directions in Familiar and Unfamiliar Environments

Abstract: Route directions are instructions, primarily verbal, that explain how to get from one place to another. The current study examines several methods for assessing the quality of verbal route directions by characterizing them in terms of the number of elements (such as landmarks, segments or turns) and by subjective ratings of their goodness. Route directions for routes which were both familiar and unfamiliar to the participant were studied. Subjective ratings of the quality of route directions were reliable and consistent across individuals. More complete route directions were rated as being of higher quality. For all routes, inclusion of more segment and turn mentions were correlated with higher quality route directions. Good route descriptions for familiar versus unfamiliar routes differed in terms of the types of landmarks included.

UMAC : Fast and secure message authentication

Abstract: We describe a message authentication algorithm, UMAC, which can authenticate messages (in software, on contemporary machines) roughly an order of magnitude faster than current practice (e.g., HMAC-SHA1), and about twice as fast as times previously reported for the universal hash-function family MMH. To achieve such speeds, UMAC uses a new universal hash-function family, NH, and a design which allows effective exploitation of SIMD parallelism The cryptographic work of UMAC is done using standard primitives of the user's choice, such as a block cipher or cryptographic hash function; no new heuristic primitives are developed here. Instead, the security of UMAC is rigorously proven, in the sense of giving exact and quantitatively strong results which demonstrate an inability to forge UMAC-authenticated messages assuming an inability to break the underlying cryptographic primitive. Unlike conventional, inherently serial MACs, UMAC is parallelizable, and will have ever-faster implementation speeds as machines offer up increasing amounts of parallelism. We envision UMAC as a practical algorithm for next-generation message authentication.

Control of fertilization-independent endosperm development by the MEDEA polycomb gene in Arabidopsis

Abstract: Higher plant reproduction is unique because two cells are fertilized in the haploid female gametophyte. Egg and sperm nuclei fuse to form the embryo. A second sperm nucleus fuses with the central cell nucleus that replicates to generate the endosperm, a tissue that supports embryo development. To understand mechanisms that initiate reproduction, we isolated a mutation in Arabidopsis, f644, that allows for replication of the central cell and subsequent endosperm development without fertilization. When mutant f644 egg and central cells are fertilized by wild-type sperm, embryo development is inhibited, and endosperm is overproduced. By using a map-based strategy, we cloned and sequenced the F644 gene and showed that it encodes a SET-domain polycomb protein. Subsequently, we found that F644 is identical to MEDEA (MEA), a gene whose maternal-derived allele is required for embryogenesis [Grossniklaus, U., Vielle-Calzada, J.-P., Hoeppner, M. A. & Gagliano, W. B. (1998) Science 280, 446–450]. Together, these results reveal functions for plant polycomb proteins in the suppression of central cell proliferation and endosperm development. We discuss models to explain how polycomb proteins function to suppress endosperm and promote embryo development.

Where it hurts: Indian material for an ethics of organ transplantation.

Abstract: This article focuses on ethical issues surrounding the selling and buying of human organs. The author argues that most people who sell their organs (mainly kidneys) in India do so in order to pay already existing debts. The transaction is only temporarily an exchange of life for life, and most donors are back in debt soon after the operation. The author discusses the flexible ethics that reduce reality to dyadic transactions and the purgatorial ethics that collapse real and imaginary exploitation in the service of complex interests. He also offers a sophisticated discussion of the ethics of publicity and public ethics. He emphasizes the lack of factual information, intentional manipulation of information, and the dissemination of kidney panics and kidney scandals, especially by the new developing bioauthorities and bioethical brokers.

Scaling up Dynamic Time Warping to Massive Dataset

Abstract: There has been much recent interest in adapting data mining algorithms to time series databases. Many of these algorithms need to compare time series. Typically some variation or extension of Euclidean distance is used. However, as we demonstrate in this paper, Euclidean distance can be an extremely brittle distance measure. Dynamic time warping (DTW) has been suggested as a technique to allow more robust distance calculations, however it is computationally expensive. In this paper we introduce a modification of DTW which operates on a higher level abstraction of the data, in particular, a piecewise linear representation. We demonstrate that our approach allows us to outperform DTW by one to three orders of magnitude. We experimentally evaluate our approach on medical, astronomical and sign language data.

The venus flytrap of periplasmic binding proteins: An ancient protein module present in multiple drug receptors

Abstract: Located between the inner and outer membranes of Gram-negative bacteria, periplasmic binding proteins (PBPs) scavenge or sense diverse nutrients in the environment by coupling to transporters or chemotaxis receptors in the inner membrane. Their three-dimensional structures have been deduced in atomic detail with the use of X-ray crystallography, both in the free and liganded state. PBPs consist of two large lobes that close around the bound ligand, resembling a Venus flytrap. This architecture is reiterated in transcriptional regulators, such as the lac repressors. In the process of evolution, genes encoding the PBPs have fused with genes for integral membrane proteins. Thus, diverse mammalian receptors contain extracellular ligand binding domains that are homologous to the PBPs; these include glutamate/glycine-gated ion channels such as the NMDA receptor, G protein-coupled receptors, including metabotropic glutamate, GABA-B, calcium sensing, and pheromone receptors, and atrial natriuretic peptide-guanylate cyclase receptors. Many of these receptors are promising drug targets. On the basis of homology to PBPs and a recently resolved crystal structure of the extracellular binding domain of a glutamate receptor ion channel, it is possible to construct three-dimensional models of their ligand binding domains. Together with the extensive information available on the mechanism of ligand binding to PBPs, such models can serve as a guide in drug discovery.

Nitrogen yields from undisturbed watersheds in the Americas

Abstract: Yields of total fixed nitrogen and nitrogen fractions are summarized for thirty-one watersheds in which anthropogenic disturbance of the nitrogen cycle, either through land use or atmospheric deposition, is negligible or slight. These yields are taken as representative of background conditions over a broad range of watershed areas, elevations, and vegetation types. The data set focuses on watersheds of the American tropics, but also includes information on the Gambia River (Africa) and some small watersheds in the Sierra Nevada of California. For the tropical watersheds, total nitrogen yield averages 5.1 kg ha -1 y-1. On average, 30% of the total is particulate and 70% is dissolved. Of the dissolved fraction, an average of 50% is organic and 50% is inorganic, of which 20% is ammonium and 80% is nitrate. Yields are substantially lower than previously estimated for background conditions. Yields of all nitrogen fractions are strongly related to runoff, which also explains a large percentage of variance in yield of total nitrogen (r2 = 0.85). For total nitrogen and nitrogen fractions, yield increases at about two-thirds the rate of runoff; concentration decreases as runoff increases. There is a secondary but significant positive relationship between elevation and yield of DIN. Ratios DONAIDN and PN/TN both are related to watershed area rather than runoff; DON/TDN decreases and PN/TN increases toward higher stream orders. The analysis suggests for tropical watersheds the existence of mechanisms promoting strong homeostasis in the yield of N and its fractions for a given moisture regime, as well as predictable downstream change in proportionate representation N fractions. Yields and concentrations for small tropical watersheds are much larger than for the few temperate ones with which comparisons are possible.

Has Cable Ended the Golden Age of Presidential Television

Abstract: For the past 30 years, presidents have enlisted prime-time television to promote their policies to the American people. For most of this era, they have been able to commandeer the national airwaves and speak to “captive” viewers. Recently, however, presidents appear to be losing their audiences. Two leading explanations are the rise of political disaffection and the growth of cable. We investigate both by developing and testing a model of the individual's viewing decision using both cross-sectional (1996 NES survey) and time-series (128 Nielsen audience ratings for presidential appearances between 1969 and 1998) data. We find that cable television but not political disaffection has ended the golden era of presidential television. Moreover, we uncover evidence that both presidents and the broadcast networks have begun adapting strategically to this new reality in scheduling presidential appearances.

Detection of biological molecules using boronate-based chemical amplification and optical sensors

Abstract: Methods are provided for the determination of the concentration of biological levels of polyhydroxylated compounds, particularly glucose. The methods utilize an amplification system that is an analyte transducer immobilized in a polymeric matrix, where the system is implantable and biocompatible. Upon interrogation by an optical system, the amplification system produces a signal capable of detection external to the skin of the patient. Quantitation of the analyte of interest is achieved by measurement of the emitted signal.

Control method and apparatus for internal combustion engine electric hybrid vehicles

Abstract: A method and apparatus for controlling the power output of an internal combustion engine in a vehicle, wherein a motor/generator or a generator/motor is coupled to the output shaft of the engine and the positive and negative torque of the motor/generator or the generator/motor is varied to control the power output of the engine as a function of speed for all manners of performance of the vehicle. The engine operates along a predetermined ideal operating line at all speeds of the vehicle.

Q-controlled microresonators and tunable electronic filters using such resonators

Abstract: Resonator systems with controlled quality factors including a resonator having a plurality of ports and a first quality factor greater than the system quality factor, and an amplifier providing negative feedback among the ports to render the system quality factor independent of the resonator quality factor.

Food Heating and the Formation of Heterocyclic Aromatic Amine and Polycyclic Aromatic Hydrocarbon Mutagens/Carcinogens

Abstract: Heterocyclic aromatic amines (HAA) and polycyclic aromatic hydrocarbons (PAH) are mutagens and animal carcinogens sometimes formed when foods are heated or processed. Determining their role in cancer etiology depends on comparing human exposures and determining any significant dose-related effect. Chemical analysis of foods shows that flame-grilling can form both PAH and HAA, and that frying forms predominantly HAA. With detection limits of about 0.1 ng/g, amounts found in commercially processed or restaurant foods range from 0.1 to 14 ng/g for HAA, and levels of PAH up to 1 ng/g in a liquid smoke flavoring. Laboratory fried samples have greater amounts of PAH, up to 38 ng/g in hamburgers, and high levels of HAA, over 300 ng/g, are measured in grilled chicken breast. Understanding the processing conditions that form PAH and HAA can lead to methods to greatly reduce their occurrence in processed foods.

A Study of the Allocation Behavior of the SPECjvm98 Java Benchmark

Abstract: We present an analysis of the memory usage for six of the Java programs in the SPECjvm98 benchmark suite. Most of the programs are real-world applications with high demands on the memory system. For each program, we measured as much low level data as possible, including age and size distribution, type distribution, and the overhead of object alignment. Among other things, we found that non-pointer data usually represents more than 50% of the allocated space for instance objects, that Java objects tend to live longer than objects in Smalltalk or ML, and that they are fairly small.

Maladaptive Behavior Differences in Prader-Willi Syndrome Due to Paternal Deletion versus Maternal Uniparental Disomy.

Abstract: Maladaptive behavior was compared across 23 people with Prader-Willi syndrome due to paternal deletion to 23 age- and gender-matched subjects with maternal uniparental disomy. Controlling for the higher IQs of the uniparental disomy group, deleted cases showed significantly higher maladaptive ratings on the Child Behavior Checklist's Internalizing, Externalizing, and Total domains as well as more symptom-related distress on the Yale-Brown Obsessive-Compulsive Scale. Across both measures, deleted cases were more apt to skin-pick, bite their nails, hoard, overeat, sulk, and withdraw. A dampening of symptom severity is suggested in Prader-Willi syndrome cases due to maternal uniparental disomy. Findings are compared to Angelman syndrome, and possible genetic mechanisms are discussed, as are implications for Prader-Willi syndrome and obsessive-compulsive behaviors.

A miniature support for thin films containing single channels or nanopores and methods for using same

Abstract: Single-channel thin film devices and methods for using the same are provided. The subject devices comprise cis and trans chambers (1 and 2) connected by an electrical communication means (3). At the cis end of the electrical communication means is a horizontal conical aperture (4) sealed with a thin film that includes a single nanopore or channel. The devices further include a means for applying an electric field between the cis and trans chambers. The subject devices find use in applications in which the ionic current through a nanopore or channel is monitored, where such applications include the characterization of naturally occurring ion channels, the characterization of polymeric compounds, and the like.

Optically generated ultrasound for enhanced drug delivery

Abstract: High frequency acoustic waves, analogous to ultrasound, can enhance the delivery of therapeutic compounds into cells. The compounds delivered may be chemotherapeutic drugs, antibiotics, photodynamic drugs or gene therapies. The therapeutic compounds are administered systemically, or preferably locally to the targeted site. Local delivery can be accomplished through a needle, cannula, or through a variety of vascular catheters, depending on the location of routes of access. To enhance the systemic or local delivery of the therapeutic compounds, high frequency acoustic waves are generated locally near the target site, and preferably near the site of compound administration. The acoustic waves are produced via laser radiation interaction with an absorbing media and can be produced via thermoelastic expansion, thermodynamic vaporization, material ablation, or plasma formation. Acoustic waves have the effect of temporarily permeabilizing the membranes of local cells, increasing the diffusion of the therapeutic compound into the cells, allowing for decreased total body dosages, decreased side effects, and enabling new therapies.

High-throughput, low-latency next generation internet networks using optical label switching and high-speed optical header generation, detection and reinsertion

Abstract: As optical signaling header technique applicable to optical networks wherein packet routing information is embedded in the same channel or wavelength as the data payload so that both the header and the data payload propagate through network elements with the same path and the associated delays. The header routing information has sufficiently different characteristics from the data payload so that the signaling header can be detected without being affected by the data payload, and that the signaling header can also be removed without affecting the data payload. The signal routing technique can overlaid onto the conventional network elements in a modular manner using two types of applique modules. The first type effects header encoding and decoding at the entry and exit points of the data payload into and out of the network; the second type effects header detection at each of the network elements.

Release mechanism utilizing shape memory polymer material

Abstract: Microfabricated therapeutic actuators are fabricated using a shape memory polymer (SMP), a polyurethane-based material that undergoes a phase transformation at a specified temperature (Tg). At a temperature above temperature Tg material is soft and can be easily reshaped into another configuration. As the temperature is lowered below temperature Tg the new shape is fixed and locked in as long as the material stays below temperature Tg. Upon reheating the material to a temperature above Tg, the material will return to its original shape. By the use of such SMP material, SMP microtubing can be used as a release actuator for the delivery of embolic coils through catheters into aneurysms, for example. The microtubing can be manufactured in various sizes and the phase change temperature Tg is determinate for an intended temperature target and intended use.

Circuit and method for eliminating surface currents on metals

Abstract: A two dimensional periodic pattern of capacitive and inductive elements (12, 14) defined in the surface of a metal sheet are provided by a plurality of conductive patches (62) each connected to a conductive back plane sheet (30) between which an insulating dielectric (26) is disposed. The elements act to suppress surface currents in the surface defined by them. In particular, the array forms a ground plane mesh (24) for use in combination with an antenna. The performance of the ground plane mesh is characterized by a frequency band within which no substantial surface currents are able to propagate along the ground plane mesh. Use of such a ground plane in aircraft or other metallic vehicles thereby prevents radiation from the antenna from propagating along the metallic skin of the aircraft or vehicle. The surface also reflects electromagnetic waves without the phase shift that occurs on a normal metal surface.

In vivo blockade of CTLA-4 enhances the priming of responsive T cells but fails to prevent the induction of tumor antigen-specific tolerance

Abstract: The efficacy of therapeutic vaccination for the treatment of cancer is limited by peripheral tolerance to tumor antigens. In vivo blockade of CTLA-4, a negative regulator of T cell function, can induce the regression of established tumors and can augment the tumor rejection achieved through therapeutic vaccination. These outcomes may reflect enhanced tumor-specific T cell priming and/or interference with the development of tolerance to tumor antigens. We examined the effect of CTLA-4 blockade on the fate and function of T cells specific for a model tumor antigen in the tumor-bearing host. We found that while CTLA-4 blockade enhanced the priming of responsive T cells, it did not prevent the induction of tolerance to tumor antigens. These results demonstrate that there is a critical window in which the combination of CTLA-4 blockade and vaccination achieves an optimal response, and they point to mechanisms other than CTLA-4 engagement in mediating peripheral T cell tolerance to tumor antigens.

Implantable medical sensor system

Abstract: An implantable chemical sensor system for medical applications is described which permits selective recognition of an analyte using an expandable biocompatible sensor, such as a polymer, that undergoes a dimensional change in the presence of the analyte. The expandable polymer is incorporated into an electronic circuit component that changes its properties (e.g., frequency) when the polymer changes dimension. As the circuit changes its characteristics, an external interrogator transmits a signal transdermally to the transducer, and the concentration of the analyte is determined from the measured changes in the circuit. This invention may be used for minimally invasive monitoring of blood glucose levels in diabetic patients.

Immune correlates of depression.

Abstract: Substantial evidence has shown that major depression is associated with immune variations. In a meta-analytic review of over thirty-five independent study samples conducted through 1991, depression was found to be associated with reliable alterations in several enumerative measures and in functional assays such as mitogen induced lymphocyte proliferation and natural killer (NK) cell activity (Herbert & Cohen, 1993a). Since 1991, many additional studies on the relationship between depression and immune measures have been published which has led to a recent reevaluation of the immune findings in depression (Zorrilla, Luborsky, McKay, Rosenthal, Houldin, Tax, McCorkle, Seligman, & Schmidt, 1998). While both reviews observed similar relations between depression and several immune measures including major immune cell classes, lymphocyte proliferation, and NK activity, conflicting results were obtained for many other measures. An enormous heterogeneity in the findings is suggested by the discrepancies between these two large meta-analytic reviews.

Averaging Expert Predictions

Abstract: We consider algorithms for combining advice from a set of experts. In each trial, the algorithm receives the predictions of the experts and produces its own prediction. A loss function is applied to measure the discrepancy between the predictions and actual observations. The algorithm keeps a weight for each expert. At each trial the weights are first used to help produce the prediction and then updated according to the observed outcome. Our starting point is Vovk's Aggregating Algorithm, in which the weights have a simple form: the weight of an expert decreases exponentially as a function of the loss incurred by the expert. The prediction of the Aggregating Algorithm is typically a non-linear function of the weights and the experts' predictions. We analyze here a simplified algorithm in which the weights are as in the original Aggregating Algorithm, but the prediction is simply the weighted average of the experts' predictions. We show that for a large class of loss functions, even with the simplified prediction rule the additional loss of the algorithm over the loss of the best expert is at most c ln n, where n is the number of experts and c a constant that depends on the loss function. Thus, the bound is of the same form as the known bounds for the Aggregating Algorithm, although the constants here are not quite as good. We use relative entropy to rewrite the bounds in a stronger form and to motivate the update.