Showing papers by "University of California published in 2000"

Assigning protein functions by comparative genome analysis protein phylogenetic profiles

Abstract: A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A′ and B′ have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A′ and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

Capital-skill complementarity and inequality: A macroeconomic analysis

Abstract: The supply and price of skilled labor relative to unskilled labor have changed dramatically over the postwar period. The relative quantity of skilled labor has increased substantially, and the skill premium, which is the wage of skilled labor relative to that of unskilled labor, has grown significantly since 1980. Many studies have found that accounting for the increase in the skill premium on the basis of observable variables is difficult and have concluded implicitly that latent skill-biased technological change must be the main factor responsible. This paper examines that view systematically. We develop a framework that provides a simple, explicit economic mechanism for understanding skill-biased technological change in terms of observable variables, and we use the framework to evaluate the fraction of variation in the skill premium that can be accounted for by changes in observed factor quantities. We find that with capital-skill complementarity, changes in observed inputs alone can account for most of the variations in the skill premium over the last 30 years.

Activity theory as a framework for analyzing and redesigning work

Abstract: Cultural-historical activity theory is a new framework aimed at transcending the dichotomies of micro- and macro-, mental and material, observation and intervention in analysis and redesign of work. The approach distinguishes between short-lived goal-directed actions and durable, object-oriented activity systems. A historically evolving collective activity system, seen in its network relations to other activity systems, is taken as the prime unit of analysis against which scripted strings of goal-directed actions and automatic operations are interpreted. Activity systems are driven by communal motives that are often difficult to articulate for individual participants. Activity systems are in constant movement and internally contradictory. Their systemic contradictions, manifested in disturbances and mundane innovations, offer possibilities for expansive developmental transformations. Such transformations proceed through stepwise cycles of expansive learning which begin with actions of questioning the existing standard practice, then proceed to actions of analyzing its contradictions and modelling a vision for its zone of proximal development, then to actions of examining and implementing the new model in practice. New forms of work organization increasingly require negotiated 'knotworking' across boundaries. Correspondingly, expansive learning increasingly involves horizontal widening of collective expertise by means of debating, negotiating and hybridizing different perspectives and conceptualizations. Findings from a longitudinal intervention study of children's medical care illuminate the theoretical arguments.

Ultra-bright source of polarization-entangled photons

Abstract: Utilizing the process of spontaneous parametric down-conversion in a novel crystal geometry, a source of polarization-entangled photon pairs has been provided that is more than ten times brighter, per unit of pump power, than previous sources, with another factor of 30 to 75 expected to be readily achievable. A high level of entanglement between photons emitted over a relatively large collection angle, and over a 10-nm bandwidth, is a characteristic of the invention. As a demonstration of the source capabilities, a 242-σ violation of Bell's inequalities was attained in fewer than three minutes, and near-perfect photon correlations were achieved when the collection efficiency was reduced. In addition, both the degree of entanglement, and the purity of the state are readily tunable. The polarization entangled photon source can be utilized as a light source for the practice of quantum cryptography.

Phase-resolved optical coherence tomography and optical doppler tomography for imaging fluid flow in tissue with fast scanning speed and high velocity sensitivity

Abstract: The invention is a fast-scanning ODT system that uses phase information derived from a Hilbert transformation to increase the sensitivity of flow velocity measurements while maintaining high spatial resolution. The significant increases in scanning speed and velocity sensitivity realized by the invention make it possible to image in vivo blood flow in human skin. The method of the invention overcomes the inherent limitations of the prior art ODT by using a phase change between sequential line scans for velocity image reconstruction. The ODT signal phase or phase shifts at each pixel can be determined from the complex function, {tilde over (Γ)}ODT(t), which is determined through analytic continuation of the measured interference fringes function, ΓODT(t), by use of a Hilbert transformation, by electronic phase demodulation, by optical means, or a fast Fourier transformation. The phase change in each pixel between axial-line scans is then used to calculate the Doppler frequency shift. Sequential measurements of a single line scan, measurements of sequential line scans or measurements of line scans in sequential frames may be used. Because the time between line scans is much longer than the pixel time window, very small Doppler shifts can be detected with this technique. In addition, spatial resolution and velocity sensitivity are decoupled. Furthermore, because two axial-line scans are compared at the same location, speckle modulations in the fringe signal cancel each other and, therefore, will not affect the phase-difference calculation.

The Global Situation

Abstract: Imagine an internet system, linking up computer users. Or a rush of immigrants across national borders. Or capital investments shuttled to varied offshore locations. These world-making "flows," too, are not just interconnections but also the recarving of channels and the remapping of the possibilities of geography. Imagine the landscape nourished by the creek. Yet even beyond the creek's "flows," there are no stable landscape elements: Trees sprout up, transforming meadows into forests; cattle browse on saplings, spreading meadows past forest edges. Nor are forests and meadows the only way to divide up the landscape. Consider the perspective of the earthworm, looking for rich soils, or the weed, able to flourish in both meadow and forest, though only when each meets certain conditions. To tell the story of this landscape requires an appreciation not only of changing landscape elements but also of the partial, tentative, and shifting ability of the storyteller to identify elements at all. Imagine ethnic groups, corporations, refugees, nongovernmental organizations (NGOs), nation-states, consumers, social movements, media moguls, trade organizations, social scientists, international lawyers, and bankers, all swarming alongside creeks and earthworms to compose the landscape, to define its elements, carve its channels of flow, and establish its units of historical agency. We live in a time of self-consciousness about units and scales: Where shall we draw the boundaries of regions? How are local communities composed? And, most important for this essay, what is this thing we call the globe? If social scientists have had a lot to say about these questions of late, so have other people. Contestants form themselves in shifting alliances, mobilized for reasons of power, passion, discipline, or dis-ease and mounting campaigns for particular configurations of scale. Some of the most excited campaigning in the last 25 years has concerned the globe, that planet-wide space for all humanity and its encompassing habitat. Moreover, in the last ten years, talk about the globe has heated up to the point that many commentators imagine a global era,

A Practical and Provably Secure Coalition-Resistant Group Signature Scheme

Abstract: A group signature scheme allows a group member to sign messages anonymously on behalf of the group However, in the case of a dispute, the identity of a signature's originator can be revealed (only) by a designated entity The interactive counterparts of group signatures are identity escrow schemes or group identification scheme with revocable anonymity This work introduces a new provably secure group signature and a companion identity escrow scheme that are significantly more efficient than the state of the art In its interactive, identity escrow form, our scheme is proven secure and coalition-resistant under the strong RSA and the decisional Diffie-Hellman assumptions The security of the noninteractive variant, ie, the group signature scheme, relies additionally on the Fiat-Shamir heuristic (also known as the random oracle model)

A practical and provably secure coalition-resistant group signature scheme

Abstract: A group signature scheme allows a group member to sign messages anonymously on behalf of the group. However, in the case of a dispute, the identity of a signature's originator can be revealed (only) by a designated entity. The interactive counterparts of group signatures are identity escrow schemes or group identification scheme with revocable anonymity. This work introduces a new provably secure group signature and a companion identity escrow scheme that are significantly more efficient than the state of the art. In its interactive, identity escrow form, our scheme is proven secure and coalition-resistant under the strong RSA and the decisional Diffie-Hellman assumptions. The security of the non-interactive variant, i.e., the group signature scheme, relies additionally on the Fiat-Shamir heuristic (also known as the random oracle model).

Is the professional satisfaction of general internists associated with patient satisfaction

Abstract: BACKGROUND: The growth of managed care has raised a number of concerns about patient and physician satisfaction. An association between physicians’ professional satisfaction and the satisfaction of their patients could suggest new types of organizational interventions to improve the satisfaction of both.

Finfet transistor structures having a double gate channel extending vertically from a substrate and methods of manufacture

Abstract: A FinFET device is fabricated using conventional planar MOSFET technology. The device is fabricated in a silicon layer overlying an insulating layer (e.g., SIMOX) with the device extending from the insulating layer as a fin. Double gates are provided over the sides of the channel to provide enhanced drive current and effectively suppress short channel effects. A plurality of channels can be provided between a source and a drain for increased current capacity. In one embodiment two transistors can be stacked in a fin to provide a CMOS transistor pair having a shared gate.

Reciprocal activation of Xenobiotic response genes by nuclear receptors SXR/PXR and CAR

Abstract: The cytochrome P450 (CYP) gene products such as CYP3A and CYP2B are essential for the metabolism of steroid hormones and xenochemicals including prescription drugs. Nuclear receptor SXR/PXR (steroid and xenobiotic receptor/pregnenolone X receptor) has been shown both biochemically and genetically to activate CYP3A genes, while similar studies have established constitutive androstane receptor (CAR) as a CYP2B regulator. The response elements in these genes are also distinct, furthering the concept of independent regulation. Unexpectedly, we found that SXR can regulate CYP2B, both in cultured cells and in transgenic mice via adaptive recognition of the phenobarbital response element (PBRE). In a type of functional symmetry, orphan receptor CAR was also found to activate CYP3A through previously defined SXR/PXR response elements. These observations not only provide a rational explanation for the activation of multiple CYP gene classes by certain xenobiotics, but also reveal the existence of a metabolic safety net that confers a second layer of protection to the harmful effects of toxic compounds and at the same time increases the propensity for drug–drug interactions.

Real Time Cryptanalysis of A5/1 on a PC

Abstract: A5/1 is the strong version of the encryption algorithm used by about 130 million GSM customers in Europe to protect the over-the-air privacy of their cellular voice and data communication. The best published attacks against it require between 240 and 245 steps. This level of security makes it vulnerable to hardware-based attacks by large organizations, but not to software-based attacks on multiple targets by hackers. In this paper we describe new attacks on A5/1, which are based on subtle flaws in the tap structure of the registers, their noninvertible clocking mechanism, and their frequent resets. After a 248 parallelizable data preparation stage (which has to be carried out only once), the actual attacks can be carried out in real time on a single PC. The first attack requires the output of the A5/1 algorithm during the first two minutes of the conversation, and computes the key in about one second. The second attack requires the output of the A5/1 algorithm during about two seconds of the conversation, and computes the key in several minutes. The two attacks are related, but use different types of time-memory tradeoffs. The attacks were verified with actual implementations, except for the preprocessing stage which was extensively sampled rather than completely executed. REMARK: We based our attack on the version of the algorithm which was derived by reverse engineering an actual GSM telephone and published at http://www.scard.org. We would like to thank the GSM organization for graciously confirming to us the correctness of this unofficial description. In addition, we would like to stress that this paper considers the narrow issue of the cryptographic strength of A5/1, and not the broader issue of the practical security of fielded GSM systems, about which we make no claims.

Flows in Stenotic Vessels

Abstract: ▪ Abstract The relationship between flow in the arteries, particularly the wall shear stresses, and the sites where atherosclerosis develops has motivated much of the research on arterial flow in recent decades. It is now well accepted that it is sites where shear stresses are low, or change rapidly in time or space, that are most vulnerable. These conditions are likely to prevail at places where the vessel is curved; bifurcates; has a junction, a side branch, or other sudden change in flow geometry; and when the flow is unsteady. These flows, often but not always involving flow separation or secondary motions, are also the most difficult ones in fluid mechanics to analyze or compute. In this article we review the modeling studies and experiments on steady and unsteady, two-and three-dimensional flows in arteries, and in arterial geometries most relevant in the context of atherosclerosis. These include studies of normal vessels—to identify, on the basis of the fluid mechanics, lesion foci—and stenotic ves...

The Lee-Carter Method for Forecasting Mortality, with Various Extensions and Applications

Abstract: In 1992, Lee and Carter published a new method for long-run forecasts of the level and age pattern of mortality, based on a combination of statistical time series methods and a simple approach to dealing with the age distribution of mortality. The method describes the log of a time series of age-specific death rates as the sum of an age-specific component that is independent of time and another component that is the product of a time-varying parameter reflecting the general level of mortality, and an age-specific component that represents how rapidly or slowly mortality at each age varies when the general level of mortality changes. This model is fit to historical data. The resulting estimate of the time-varying parameter is then modeled and forecast as a stochastic time series using standard methods. From this forecast of the general level of mortality, the actual age-specific rates are derived using the estimated age effects. The forecasts of the various life table functions have probability di...

Process for forming shaped group II-VI semiconductor nanocrystals, and product formed using process

Abstract: A process for the formation of shaped Group II-VI semiconductor nanocrystals comprises contacting the semiconductor nanocrystal precursors with a liquid media comprising a binary mixture of phosphorus-containing organic surfactants capable of promoting the growth of either spherical semiconductor nanocrystals or rod-like semiconductor nanocrystals, whereby the shape of the semiconductor nanocrystals formed in said binary mixture of surfactants is controlled by adjusting the ratio of the surfactants in the binary mixture.

Physical activity for the chronically ill and disabled.

Abstract: Exercise prescription principles for persons without chronic disease and/or disability are based on well developed scientific information. While there are varied objectives for being physically active, including enhancing physical fitness, promoting health by reducing the risk for chronic disease and ensuring safety during exercise participation, the essence of the exercise prescription is based on individual interests, health needs and clinical status, and therefore the aforementioned goals do not always carry equal weight. In the same manner, the principles of exercise prescription for persons with chronic disease and/or disability should place more emphasis on the patient's clinical status and, as a result, the exercise mode, intensity, frequency and duration are usually modified according to their clinical condition. Presently, these exercise prescription principles have been scientifically defined for clients with coronary heart disease. However, other diseases and/or disabilities have been studied less (e.g. renal failure, cancer, chronic fatigue syndrome, cerebral palsy). This article reviews these issues with specific reference to persons with chronic diseases and disabilities.

The Networked Polity: Regional Development in Western Europe

Abstract: Drawing together work in comparative politics, public administration, organization theory, and economic sociology, this article describes a distinctive form of modern polity-the ‘networked polity’. In the networked polity, states are strongly embedded in society and pursue their objectives by operating through networks of societal associations. Both state agencies and societal associations take the form of ‘network’ or ‘organic’ organizations-decentralized, team-based organizations with strong lateral communication and coordination that crosses functional boundarieswithin and between organizations. These organizations are then linked together by means of cooperative exchange relationships around common projects. The role of the state is to empower stakeholders and facilitate cooperation among them. The concept is illustrated through an examination of regional development strategies in Western Europe.

Adhesive microstructure and method of forming same

Abstract: A method of forming an adhesive force includes removing a seta from a living specimen, attaching the seta to a substrate, and applying the seta to a surface so as to establish an adhesive force between the substrate and the surface. The seta is applied to the surface with a force perpendicular to the surface. The seta is then pulled with a force parallel to the surface so as to preload the adhesive force of the seta.

Authentic Third-party Data Publication

Abstract: Integrity critical databases, such as financial data used in high-value decisions, are frequently published over the Internet. Publishers of such data must satisfy the integrity, authenticity, and non-repudiation requirements of clients. Providing this protection over public networks is costly.

The consumer revolution in urban China

Abstract: List of Figures and Table Acknowledgements 1. Introduction: A Revolution in Consumption, by Deborah S. Davis 2. Inventing Oasis: Luxury Housing Advertisements in Reconfiguring Domestic Space in Shanghai, by David Fraser 3. Commercializing Childhood: Parental Purchases for Shanghai's Only Child, by Deborah S. Davis and Julia S. Sensenbrenner 4. What's in a Dress? Brides in the Hui Quarter of Xi'an, by Maris Gillette 5. The Revitalization of the Marketplace: Food Markets of Nanjing, by Ann Veeck 6. To Be Relatively Comfortable in an Egalatarian Society, by Hanlong Lu 7. Heart-to-Heart, Phone-to-Phone: Family Values, Sexuality, and the Politics of Shanghai's Advice Hotlines, by Kathleen Erwin 8. Greeting Cards in China: Mixed Language in Connections and Affections, by Mary S. Erbaugh 9. Of Hamburger and Social Space: Consuming McDonald's in Beijing, by Yunxiang Yan 10. Dancing through the Market Transition: Disco and Dance Hall Sociability in Shanghai, by James Farrer 11. Cultivating Friendship through Bowling in Shenzhen, by Gan Wang 12. Cigarettes and Domination in Chinese Business Networks: Institutional Change during the Market Transition, by David L. Wank 13. Public Monuments and Private Pleasures in the Parks of Nanjing: A Tango in the Ruins of the Ming, by Richard Kraus 14. Epilogue: The Second Liberation, by Richard Madsen Contributors Bibliography Index

A Simple Dimensionality Reduction Technique for Fast Similarity Search in Large Time Series Databases

Abstract: We address the problem of similarity search in large time series databases. We introduce a novel-dimensionality reduction technique that supports an indexing algorithm that is more than an order of magnitude faster than the previous best known method. In addition to being much faster our approach has numerous other advantages. It is simple to understand and implement, allows more flexible distance measures including weighted Euclidean queries and the index can be built in linear time. We call our approach PCA-indexing (Piece-wise Constant Approximation) and experimentally validate it on space telemetry, financial, astronomical, medical and synthetic data.

Designing the Knowledge Integration Environment

Abstract: The Knowledge Integration Environment (KIE) activities were designed to promote lifelong science learning. This paper describes the partnership process that guided the design as well as the Scaffolded Knowledge Integration framework that gave the partnership a head start on creating effective materials. KIE activities take advantage of internet materials to engage students in debate of science questions like 'how far does light go?', to make scientifically oriented design decisions, and to critique science claims in the popular press. Other papers in this collection describe the design studies carried out to improve KIE activities. These studies have implications for improving the Scaffolded Knowledge Integration framework and can inform future designers of science instruction.

The collection of pollen by bees

Abstract: Bees require pollen for their reproduction and pollen comprises the basic larval food for bees. Most bees acquire pollen passively during flower visitation, but female bees may also collect pollen actively with the aid of various structural and behavioral adaptations. Most bees have evolved adaptations to concentrate pollen into discrete loads and transport pollen back to their nests. The various structural and behavioral adaptations of female bees for acquiring and transporting pollen are the basis of this review.

The Fossil Record: Tracing the Roots of the Cyanobacterial Lineage

Abstract: Since the mid-1960s, following a century of unrewarded search, impressive progress has been made toward deciphering the Precambrian fossil record, evidence of life extant during the earliest seven-eighths of geologic time. Hundreds of fossiliferous units have been discovered containing thousands of microbial fossils—dominantly but not exclusively cyanobacterial — and the documented antiquity of life has been extended to an age roughly three-quarters that of the Earth. Mutually reinforcing lines of evidence, paleontological, geological, and isotopic geochemical, indicate that stromatoliticmicrobial ecosystems,evidently including cyanobacteria and other members of the bacterial domain, were extant ~3500 Ma ago; methanogenic archaeans by ~2800 Ma ago; and Gram-negative sulfate-reducing bacteria at least as early as ~2700 Ma ago.The discrepancy between these dates and those suggested for emergence of these groups by a recently proposed amino acid-based “molecular clock” is too great and too consistent to be ignored. The challengeis to unify the molecular data with the increasingly well-established paleobiologicrecord.

Runtime Support for Type-Safe Dynamic Java Classes

Abstract: Modern software must evolve in response to changing conditions. In the most widely used programming environments, code is static and cannot change at runtime. This poses problems for applications that have limited down-time. More support is needed for dynamic evolution. In this paper we present an approach for supporting dynamic evolution of Java programs. In this approach, Java programs can evolve by changing their components, namely classes, during their execution. Changes in a class lead to changes in its instances, thereby allowing evolution of both code and state. The approach promotes compatibility with existing Java applications, and maintains the security and type safety controls imposed by Java's dynamic linking mechanism. Experimental analyses of our implementation indicate that the implementation imposes a moderate performance penalty relative to the unmodified virtual machine.

Simultaneous Confidence Bands and Hypothesis Testing in Varying-coefficient Models

Abstract: Regression analysis is one of the most commonly used techniques in statistics. When the dimension of independent variables is high, it is difficult to conduct efficient non- parametric analysis straightforwardly from the data. As an important alternative to the additive and other non-parametric models, varying-coefficient models can reduce the modelling bias and avoid the "curse of dimensionality" significantly. In addition, the coeffi- cient functions can easily be estimated via a simple local regression. Based on local poly- nomial techniques, we provide the asymptotic distribution for the maximum of the normalized deviations of the estimated coefficient functions away from the true coefficient functions. Using this result and the pre-asymptotic substitution idea for estimating biases and variances, simultaneous confidence bands for the underlying coefficient functions are constructed. An important question in the varying coefficient models is whether an estimated coefficient function is statistically significantly different from zero or a constant. Based on newly derived asymptotic theory, a formal procedure is proposed for testing whether a particular parametric form fits a given data set. Simulated and real-data examples are used to illustrate our techniques.

Core Elements of Digital Gazetteers: Placenames, Categories, and Footprints

Abstract: The core elements of a digital gazetteer are the placename itself, the type of place it labels, and a geographic footprint representing its location and possibly its extent. Such gazetteer data is an important component of indirect geographic referencing through placenames. Based on the gazetteer development work of the Alexandria Digital Library, this paper presents the nature of placenames, and the process of assigning categories to places based on the words in the placenames and other information, and discusses the nature of georeferencing places with geographic footprints.

Polycrystalline silicon germanium films for forming micro-electromechanical systems

Abstract: This invention relates to micro-electromechanical systems using silicon-germanium films. The invention features a process for forming a micro-electromechanical system on a substrate. This process includes depositing a sacrificial layer of silicon-germanium onto the substrate; depositing a structural layer of silicon-germanium onto the sacrificial layer, where the germanium content of the sacrificial layer is greater than the germanium content of the structural layer; and removing a portion of the sacrificial layer. A MEMS resonator (105) as seen in figure 1B can be produced by the present invention.

System and method for integrating and accessing multiple data sources within a data warehouse architecture

Abstract: A system and method is disclosed for integrating and accessing multiple data sources within a data warehouse architecture. The metadata formed by the present method provide a way to declaratively present domain specific knowledge, obtained by analyzing data sources, in a consistent and useable way. Four types of information are represented by the metadata: abstract concepts, databases, transformations and mappings. A mediator generator automatically generates data management computer code based on the metadata. The resulting code defines a translation library and a mediator class. The translation library provides a data representation for domain specific knowledge represented in a data warehouse, including “get” and “set” methods for attributes that call transformation methods and derive a value of an attribute if it is missing. The mediator class defines methods that take “distinguished” high-level objects as input and traverse their data structures and enter information into the data warehouse.

Controlled electroporation and mass transfer across cell membranes

Abstract: Electroporation is performed in a controlled manner in either individual or multiple biological cells or biological tissue by monitoring the electrical impedance, defined herein as the ratio of current to voltage in the electroporation cell. The impedance detects the onset of electroporation in the biological cell(s), and this information is used to control the intensity and duration of the voltage to assure that electroporation has occurred without destroying the cell(s). This is applicable to electroporation in general. In addition, a particular method and apparatus are disclosed in which electroporation and/or mass transfer across a cell membrane are accomplished by securing a cell across an opening in a barrier between two chambers such that the cell closes the opening. The barrier is either electrically insulating, impermeable to the solute, or both, depending on whether pore formation, diffusive transport of the solute across the membrane, or both are sought. Electroporation is achieved by applying a voltage between the two chambers, and diffusive transport is achieved either by a difference in solute concentration between the liquids surrounding the cell and the cell interior or by a differential in concentration between the two chambers themselves. Electric current and diffusive transport are restricted to a flow path that passes through the opening.