Showing papers by "University of California published in 1996"

Learning Bayesian Networks is NP-Complete

Abstract: Algorithms for learning Bayesian networks from data have two components: a scoring metric and a search procedure. The scoring metric computes a score reflecting the goodness-of-fit of the structure to the data. The search procedure tries to identify network structures with high scores. Heckerman et al. (1995) introduce a Bayesian metric, called the BDe metric, that computes the relative posterior probability of a network structure given data. In this paper, we show that the search problem of identifying a Bayesian network—among those where each node has at most K parents—that has a relative posterior probability greater than a given constant is NP-complete, when the BDe metric is used.

VIS: A System for Verification and Synthesis

Abstract: ion Manual abstraction can be performed by giving a file containing the names of variables to abstract. For each variable appearing in the file, a new primary input node is created to drive all the nodes that were previously driven by the variable. Abstracting a net effectively allows it to take any value in its range, at every clock cycle. Fair CTL model checking and language emptiness check VIS performs fair CTL model checking under Buchi fairness constraints. In addition, VIS can perform language emptiness checking by model checking the formula EG true. The language of a design is given by sequences over the set of reachable states that do not violate the fairness constraint. The language emptiness check can be used to perform language containment by expressing the set of bad behaviors as another component of the system. If model checking or language emptiness fail, VIS reports the failure with a counterexample, (i.e., behavior seen in the system that does not satisfy the property for model checking, or valid behavior seen in the system for language emptiness). This is called the “debug” trace. Debug traces list a set of states that are on a path to a fair cycle and fail the CTL formula. Equivalence checking VIS provides the capability to check the combinational equivalence of two designs. An important usage of combinational equivalence is to provide a sanity check when re-synthesizing portions of a network. VIS also provides the capability to test the sequential equivalence of two designs. Sequential verification is done by building the product finite state machine, and checking whether a state where the values of two corresponding outputs differ, can be reached from the set of initial states of the product machine. If this happens, a debug trace is provided. Both combinational and sequential verification are implemented using BDD-based routines. Simulation VIS also provides traditionaldesign verification in the form of a cycle-based simulator that uses BDD techniques. Since VIS performs both formal verification and simulation using the same data structures, consistency between them is ensured. VIS can generate random input patterns or accept user-specified input patterns. Any subtree of the specified hierarchy may be simulated.

Effect of Quantum-Well Structures on the Thermoelectric Figure of Merit in the Si/Si1-xGex System

Abstract: The Si/Si1-xGex quantum well system is attractive for high temperature thermoelectric applications and for demonstration of proof-of-principle for enhanced thermoelectric figure of merit Z, since the interfaces and carrier densities can be well controlled in this system. We report theoretical calculations for Z in this system, based on which Si/Si1-xGex quantum-well structures were grown by molecular-beam epitaxy. Thermoelectric and other transport measurements were made, indicating that an increase in Z over bulk values is possible through quantum confinement effects in the Si/Si1-xGex quantum-well structures.

Characterization of individual polymer molecules based on monomer-interface interactions

Abstract: The invention relates to a method for detecting a double-stranded region in a nucleic acid by (1) providing two separate, adjacent pools of a medium and a interface between the two pools, the interface having a channel so dimensioned as to allow sequential monomer-by-monomer passage of a single-stranded nucleic acid, but not of a double-stranded nucleic acid, from one pool to the other pool; (2) placing a nucleic acid polymer in one of the two pools; and (3) taking measurements as each of the nucleotide monomers of the single-stranded nucleic acid polymer passes through the channel so as to differentiate between nucleotide monomers that are hybridized to another nucleotide monomer before entering the channel and nucleotide monomers that are not hybridized to another nucleotide monomer before entering the channel.

Methods for drug screening

Abstract: Methods and compositions for estimating the physiological specificity of a candidate drug involve: (a) detecting reporter gene product signals from each of a plurality of different, separately isolated cells of a target organism, wherein each cell contains a recombinant construct comprising a reporter gene operatively linked to a different endogenous transcriptional regulatory element of the target organism such that the transcriptional regulatory element regulates the expression of the reporter gene, and the sum of the cells comprises an ensemble of the transcriptional regulatory elements of the organism sufficient to model the transcriptional responsiveness of said organism to a drug; (b) contacting each cell with a candidate drug; (c) detecting reporter gene product signals from each cell; (d) comparing reporter gene product signals from each cell before and after contacting the cell with the candidate drug to obtain a drug response profile which provides an estimate of the physiological specificity of the candidate drug.

Blockade of t lymphocyte down-regulation associated with ctla-4 signaling

Abstract: T cell activation in response to antigen is increased by the administration of binding agents that block CTLA-4 signaling. When CTLA-4 signaling is thus blocked, the T cell response to antigen is released from inhibition. Such an enhanced response is useful for the treatment of tumors, chronic viral infections, and as an adjuvant during immunization.

Knowledge representation in fuzzy logic

Abstract: The conventional approaches to knowledge representation, e.g., semantic networks, frames, predicate calculus and Prolog, are based on bivalent logic. A serious shortcoming of such approaches is their inability to come to grips with the issue of uncertainty and imprecision. As a consequence, the conventional approaches do not provide an adequate model for modes of reasoning which are approximate rather than exact. Most modes of human reasoning and all of commonsense reasoning fall into this category.

Phoenix Risen: The Resurrection of Global Finance

Abstract: Of all the many changes of the world economy since World War II, few have been nearly so dramatic as the resurrection of global finance. A review of five recent books suggests considerable diversity of opinion concerning both the causes and the consequences of financial globalization, leaving much room for further research. Competing historical interpretations, stressing the contrasting roles of market forces and government policies, need to be reexamined for dynamic linkages among the variables they identify. Likewise, impacts on state policy at both the macro and micro levels should be explored more systematically to understand not just whether constraints may be imposed on governments but also how and under what conditions, and what policymakers can do about them. Finally, questions are also raised about implications for the underlying paradigm conventionally used for the study of international political economy and international relations more generally.

Method and apparatus for fabricating self-assembling microstructures

Abstract: A method and apparatus for assembling microstructures onto a substrate through fluid transport. The microstructures being shaped blocks self-align into recessed regions located on a substrate such that the microstructure becomes integral with the substrate. The improved method includes a step of transferring the shaped blocks into a fluid to create a slurry. Such slurry is then dispensed evenly or circulated over the top surface of a substrate having recessed regions thereon. The microstructure via the shape and fluid tumbles onto the surface of the substrate, self-aligns, and engages into a recessed region.

Silicon-based sleeve devices for chemical reactions

Abstract: A silicon-based sleeve type chemical reaction chamber (41) that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The reaction chamber combines a critical ratio of silicon and silicon nitride to the volume of material to be heated (e.g., a liquid) in order to provide uniform heating, yet low power requirements. The reaction chamber will also allow the introduction of a secondary tube (45) (e.g., plastic) into the reaction sleeve that contains the reaction mixture thereby alleviating any potential materials incompatibility issues. The reaction chamber may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The reaction chamber may be used in synthesis instruments, particularly those for DNA amplification and synthesis.

Determination of Protein Secondary Structure

Abstract: Circular dichroism (CD) is one of the most sensitive physical techniques for determining structures and monitoring structural changes of biomolecules. It can directly interpret the changes of protein secondary structure, even though the method is empirical. The far-ultraviolet (far-UV) CD specra (below 250 nm) of proteins are extremely sensitive toward protein structure, and the near-UV spectra reflect the contributions of aromatic side chains, disulfide bonds, and induced CD bands of prosthetic groups. Together these measurements provide information about the overall structure of a protein molecule as well as its local conformation around the aromatic and prosthetic groups and disulfide linkages. The ease of CD measurements is attractive, but CD, unlike two other powerful techniques—x-ray diffraction of protein crystals and NMR for protein solutions—cannot determine the three-dimensional structure of a protein. In this chapter we will discuss several methods of CD analysis of proteins, which can provide estimates of α helix, β sheet, β turn, and unordered form. These empirical methods utilize a set of reference proteins of known structure from x-ray diffraction studies. Thus, proteins are presumed to have the same structure in the crystalline state and in aqueous solution.

Bounded scheduling of process networks

Abstract: We present a scheduling policy for complete, bounded execution of Kahn process network programs. A program is a set of processes that communicate through a network of first-in first-out queues. In a complete execution, the program terminates if and only if all processes block attempting to consume data from empty communication channels. We are primarily interested in programs that operate on infinite streams of data and never terminate. In a bounded execution, the number of data elements buffered in each of the communication channels remains bounded. The Kahn process network model of computation is powerful enough that the questions of termination and bounded buffering are undecidable. No finite-time algorithm can decide these questions for all Kahn process network programs. Fortunately, because we are interested in programs that never terminate, our scheduler has infinite time and can guarantee that programs execute forever with bounded buffering whenever possible. Our scheduling policy has been implemented using Ptolemy, an object-oriented simulation and prototyping environment.

Diffusion in Disordered Media

Abstract: We study the transport properties of a large system of interacting parti­cles moving on an integer lattice in the presence of a random field. This article contains a description of the problem, a survey of results, and an outline of our method. The results include variational formulas for the transport coefficients. The details of the proof of the hydrodynamic limit can be found in [15].

Scanning tip microwave near field microscope

Abstract: A microwave near field microscope has a novel microwave probe structure wherein the probing field of evanescent radiation is emitted from a sharpened metal tip instead of an aperture or gap. This sharpened tip, which is electrically and mechanically connected to a central electrode, extends through and beyond an aperture in an endwall of a microwave resonating device such as a microwave cavity resonator or a microwave stripline resonator. Since the field intensity at the tip increases as the tip sharpens, the total energy which is radiated from the tip and absorbed by the sample increases as the tip sharpens. The result is improved spatial resolution without sacrificing sensitivity.

Identification of a novel selD homolog from Eukaryotes, Bacteria, and Archaea: Is there an autoregulatory mechanism in selenocysteine metabolism?

Abstract: Escherichia coli selenophosphate synthetase (SPS, the selD gene product) catalyzes the production of monoselenophosphate, the selenium donor compound required for synthesis of selenocysteine (Sec) and seleno-tRNAs. We report the molecular cloning of human and mouse homologs of the selD gene, designated Sps2 , which contains an in-frame TGA codon at a site corresponding to the enzyme’s putative active site. These sequences allow the identification of selD gene homologs in the genomes of the bacterium Haemophilus influenzae and the archaeon Methanococcus jannaschii , which had been previously misinterpreted due to their in-frame TGA codon. Sps2 mRNA levels are elevated in organs previously implicated in the synthesis of selenoproteins and in active sites of blood cell development. In addition, we show that Sps2 mRNA is up-regulated upon activation of T lymphocytes and have mapped the Sps2 gene to mouse chromosome 7. Using the mouse gene isolated from the hematopoietic cell line FDCPmixA4, we devised a construct for protein expression that results in the insertion of a FLAG tag sequence at the N terminus of the SPS2 protein. This strategy allowed us to document the readthrough of the in-frame TGA codon and the incorporation of 75 Se into SPS2. These results suggest the existence of an autoregulatory mechanism involving the incorporation of Sec into SPS2 that might be relevant to blood cell biology. This mechanism is likely to have been present in ancient life forms and conserved in a variety of living organisms from all domains of life.

Numerical simulations of dynamic crack growth along an interface

Abstract: Dynamic crack growth is analyzed numerically for a plane strain bimaterial block with an initial central crack. The material on each side of the bond line is characterized by an isotropic hyperelastic constitutive relation. A cohesive surface constitutive relation is also specified that relates the tractions and displacement jumps across the bond line and that allows for the creation of new free surface. The resistance to crack initiation and the crack speed history are predicted without invoking any ad hoc failure criterion. Full finite strain transient analyses are carried out, with two types of loading considered; tensile loading on one side of the specimen and crack face loading. The crack speed history and the evolution of the crack tip stress state are investigated for parameters characterizing a PMMA/Al bimaterial. Additionally, the separate effects of elastic modulus mismatch and elastic wave speed mismatch on interface crack growth are explored for various PMMA-artificial material combinations. The mode mixity of the near tip fields is found to increase with increasing crack speed and in some cases large scale contact occurs in the vicinity of the crack tip. Crack speeds that exceed the smaller of the two Rayleigh wave speeds are also found.

Method and apparatus for optical Doppler tomographic imaging of fluid flow velocity in highly scattering media

Abstract: Optical Doppler tomography permits imaging of fluid flow velocity in highly scattering media. The tomography system combines Doppler velocimetry with high spatial resolution of partially coherent optical interferometry to measure fluid flow velocity at discrete spatial locations. Noninvasive in vivo imaging of blood flow dynamics and tissue structures with high spatial resolutions of the order of 2 to 10 microns is achieved in biological systems. The backscattered interference signals derived from the interferometer may be analyzed either through power spectrum determination to obtain the position and velocity of each particle in the fluid flow sample at each pixel, or the interference spectral density may be analyzed at each frequency in the spectrum to obtain the positions and velocities of the particles in a cross-section to which the interference spectral density corresponds. The realized resolutions of optical Doppler tomography allows noninvasive in vivo imaging of both blood microcirculation and tissue structure surrounding the vessel which has significance for biomedical research and clinical applications.

Principles of Digital Design

Abstract: (NOTE: Each chapter ends with a summary, problems and further readings.) 1. Introduction. Design representation. Levels of abstraction. Design process. CAD tools. Typical design process. Road map. 2. Data Types and Representations. Positional number systems. Octal and hexadecimal numbers. Number system conversions. Addition and subtraction of binary numbers. Representation of negative numbers. Two's-complement addition and subtraction. Binary ultiplication. Binary division. Floating-point number representation. Binary codes for decimal numbers. Character codes. Codes for error detection and correction. Hamming codes. 3. Boolean Algebra and Logic Design. Algebraic properties. Axiomatic definition of boolean algebra. Basic theorems of boolean algebra. Boolean functions. Canonical forms. Standard forms. Digital logic gates. Extension to multiple inputs and multiple operators. Gate implementations. VLSI technology. 4. Simplification of Boolean Functions. The map representation. The map method of simplification. Don't-care conditions. The tabulation method. Technology mapping for gate arrays. Technology mapping for custom libraries. Hazard-free design. 5. Combinatorial Components. Carry-ripple adders. Carry-look-ahead adders. Adders/subtractors. Logic unit. Arithmetic-Logic Unit. Decoders. Selectors. Buses. Priority encoders. Magnitude comparators. Shifters and rotators. Read-Only memories. Programmable logic arrays. 6. Sequential Logic. SR-latch. Gated SR-latch. Gated D-latch. Flip-flops. Flip-flop types. Analysis of sequential logic. Finite-state-machine model. Synthesis of sequential logic. FSM model capture. State minimization. State encoding. Choice of memory elements. Optimization and timing. 7. Storage Components. Registers. Shift registers. Counters. BCD counter. Asynchronous counter. Register files. Random-access memories (RAMs). Push-down stacks. Firs- in-first-out queue. Simple datapaths. General datapaths. Control unit design. 8. Register-Transfer Design. Design model. FSMD definition. Algorithmic-state-machine charts. Synthesis from ASM charts. Register sharing (variable merging). Functional unit sharing (operator sharing). Bus sharing (connection merging). Register merging. Chaining and multicycling. Functional unit pipelining. ASM pipelining. Control- pipelining. Scheduling. 9. Processor Design. Instruction sets. Addressing modes. Processor design. Instruction set design. Processor design. Reduced instruction set. RISC Design. Data forwarding. Branch prediction.

A Top-Down, Constraint-Driven Design Methodology for Analog Integrated Circuits

Abstract: This paper describes a top-down, constraint-driven design methodology for analog integrated circuits. Some of the tools that support this methodology are described. These include behavioral simulation tools, tools for physical assembly, and module generators. Finally, examples of behavioral simulation with optimization and physical assembly are provided to better illustrate the methodology and its integration with the tool set.

Maskless, reticle-free, lithography

Abstract: A lithography system in which the mask or reticle, which usually carries the pattern to be printed onto a substrate, is replaced by a programmable array of binary (i.e. on/off) light valves or switches which can be programmed to replicate a portion of the pattern each time an illuminating light source is flashed. The pattern of light produced by the programmable array is imaged onto a lithographic substrate which is mounted on a scanning stage as is common in optical lithography. The stage motion and the pattern of light displayed by the programmable array are precisely synchronized with the flashing illumination system so that each flash accurately positions the image of the pattern on the substrate. This is achieved by advancing the pattern held in the programmable array by an amount which corresponds to the travel of the substrate stage each time the light source flashes. In this manner the image is built up of multiple flashes and an isolated defect in the array will only have a small effect on the printed pattern. The method includes projection lithographies using radiation other than optical or ultraviolet light. The programmable array of binary switches would be used to control extreme ultraviolet (EUV), x-ray, or electron, illumination systems, obviating the need for stable, defect free masks for projection EUV, x-ray, or electron, lithographies.

Traffic scheduling system and method for packet-switched networks

Abstract: A traffic scheduling system and method for packet-switched communications networks where multiple sessions share an outgoing communications link. Prior to transmission on the outgoing link, packets are assigned a time-stamp and placed into a priority queue in order of ascending time-stamps so that the packet with the smallest time-stamp is placed at the head of the queue. The time-stamp assigned to a particular packet is calculated as the estimated time at which the last bit of the packet is transmitted in an ideal system, using a global variable called the system potential which tracks the progress of work in the scheduling system. The system potential is recalibrated periodically to avoid any long-term unfairness in service offered to the sessions sharing the outgoing link.

Organically-functionalized monodisperse nanocrystals of metals

Abstract: Organically-functionalized metal nanoparticles are produced by mixing a metal precursor with an organic surface passivant and reacting the resulting mixture with a reducing agent to generate free metal while binding the passivant to the surface of the free metal to produce organically functionalized metal particles.

Detection of transmembrane potentials by optical methods

Abstract: Methods and compositions are provided for detecting changes in membrane potential in membranes biological systems. In one aspect, the method comprises: a) providing a living cell with a first reagent comprising a charged hydrophobic molecule which is typically a fluorescence resonance energy transfer (FRET) acceptor or donor, or is a quencher and is capable of redistributing within the membrane of a biological membrane in response to changes in the potential across the membrane; b) providing the cell with a second reagent that can label the first face or the second face of a biological membrane within the cell; c) detecting light emission from the first reagent or the second reagent. One aspect of this method involves monitoring membrane potential changes in subcellular organelle membranes in a living cell. Another aspect of the invention is the use of certain embodiments of the method for the screening of test chemicals for activity to modulate the activity of a target ion channel. Another aspect of the present invention is a transgenic organism comprising a first reagent that comprises a charged hydrophobic fluorescent molecule, and a second reagent comprising a bioluminescent or naturally fluorescent protein.

Nanostructure multilayer dielectric materials for capacitors and insulators

Abstract: A capacitor is formed of at least two metal conductors having a multilayer dielectric and opposite dielectric-conductor interface layers in between. The multilayer dielectric includes many alternating layers of amorphous zirconium oxide (ZrO 2 ) and alumina (Al 2 O 3 ). The dielectric-conductor interface layers are engineered for increased voltage breakdown and extended service life. The local interfacial work function is increased to reduce charge injection and thus increase breakdown voltage. Proper material choices can prevent electrochemical reactions and diffusion between the conductor and dielectric. Physical vapor deposition is used to deposit the zirconium oxide (ZrO 2 ) and alumina (Al 2 O 3 ) in alternating layers to form a nano-laminate.

Automatic generation of functional vectors using the extended finite state machine model

Abstract: We present a method of automatic generation of functional vectors for sequential circuits. These vectors can be used for design verification, manufacturing testing, or power estimation. A high-level description of the circuit in VHDL or C is assumed available. Our method automatically transforms the high-level description of a circuit in VHDL or C into an extended finite state machine (EFSM) model that is used to generate functional vectors. The EFSM model is a generalization of the traditional state machine model. It is a compact representation of models with local data variables and preserves many nice properties of a traditional state machine model. The theoretical background of the EFSM model is addressed in this article. Our method guarantees that the generated vectors cover every statement in the high-level description at least once. Experimental results show that a set of comprehensive functional vectors for sequential circuits with more than a hundred flip-flops can be generated automatically in a few minutes of CPU time using our prototype system.

Method of fabricating boron containing coatings

Abstract: Hard coatings are fabricated from boron nitride, cubic boron nitride, and multilayer boron/cubic boron nitride, and the fabrication thereof involves magnetron sputtering in a selected atmosphere. These hard coatings may be applied to tools and engine and other parts, as well to reduce wear on tribological surfaces and electronic devices. These boron coatings contain no morphological growth features. For example, the boron is formed in an inert (e.g. argon) atmosphere, while the cubic boron nitride is formed in a reactive (e.g. nitrogen) atmosphere. The multilayer boron/cubic boron nitride, is produced by depositing alternate layers of boron and cubic boron nitride, with the alternate layers having a thickness of 1 nanometer to 1 micrometer, and at least the interfaces of the layers may be discrete or of a blended or graded composition.

Microfabricated filter with specially constructed channel walls, and containment well and capsule constructed with such filters

Abstract: Microfabricated filters utilizing a bulk substrate structure and a thin film structure and a method for constructing such filters The pores of the filters are defined by spaces between the bulk substrate structure and the thin film structure and are of substantially uniform width, length and distribution The width of the pores is defined by the thickness of a sacrificial layer and therefore may be smaller than the limit of resolution obtainable with photolithography The filters provide enhanced mechanical strength, chemical inertness, biological compatibility, and throughput The filters are constructed using relatively simple fabrication techniques Also, microfabricated containment wells and capsules constructed with such filters for the immunological isolation of cell transplants and a method for constructing such containment wells and capsules The pores of the wells and capsules are large enough to let a desired biologically-active molecular product through, while blocking the passage of all larger immunological molecules The containment wells and capsules provide enhanced biological compatibility and useful life

Novel high affinity human antibodies to tumor antigens

Abstract: This invention provides for novel human antibodies that specifically bind to c-erbB-2. The antibodies may be used alone or as components of chimeric molecules that specifically target and deliver effector molecules to cells overexpressing c-erbB-2.