A hands-free interactive reading device for people with severe paralysis. (more...)

Researchers at the University of California, Irvine have developed a software program that automatically processes and analyzes a voice and provides a score on the severity of the voice’s stutter on a real-time basis. (more...)

UC San Diego researchers studied how large or distributed solar power plants can reduce the cloud-induced variability in power output. Geographic diversity mitigates large short-term cloud cover changes, effectively smoothing total solar power output. (more...)

With the cost of sequencing the human genome dropping exponentially it will soon be economical for individuals to get the results of paternity tests, personal medicine analyses and even genetic matching or compatibility tests without the expense or trouble of elaborate laboratory procedures. Additionally, researchers from UCI’s Genomics and Computer Science departments have developed a safe and secure methodology and infrastructure to conduct these tests, safely and securely and all done via mobile devices. (more...)

UC Researchers have developed a Field-Programmable-Gate-Array (FPGA) based hardware implementation that utilizes the FM-Index for exact pattern matching for string searching.  This method of FM-Index string matching has a higher effective throughput than brute force due to the higher number of character comparisons per cycle performed by the FM-Index.  Further, the speed of this method is in the order of two orders of magnitude greater than Bowtie software tools and ten to seventy times faster than the traditional method using FHAST.   (more...)

Recent brain-computer interface (BCI) studies have demonstrated the feasibility of using electroencephalogram (EEG) to enhance human performance. For example, event-related potentials (ERP) could be used to accelerate visual target detection using a rapid serial visual presentation paradigm. However, in some environments where real-time operation is critical, current BCIs would fail to make a rapid and accurate prediction of behavior based on single-trial EEG. Under this circumstance, assessing collaborative event-related EEG activities from multiple subjects may provide a solution. (more...)

A local relaxation method for estimating optical flow using a Poisson equation. The convergence speed is faster than that obtained through conventional technology. (more...)

Disclosed here is a web-based multi-player game that has been designed to collect semantic information about songs. Players listen to clips of music and select words that describe the music. Players are assigned points based on how well their selections match those of the other players. By playing our game, users generate `annotations’ that can be used for music retrieval systems, music recommendation systems, automatic playlist generation and music knowledge discovery. (more...)

In general, microscope users manually sample fields from a specimen by observing the specimen through microscope oculars and then selecting a representative field of the specimen to image. The parameters for the image acquisition are then set, and the image is acquired and saved. This process is then repeated for a small number of additional fields manually sampled by the microscope user. This general workflow is problematic for several reasons: 1) Conventional operation of a microscope as described above is often very time consuming and does not scale well with increasing demands on throughput, 2) Most microscopes are left unused when users are not available to manually operate them, and they could otherwise be left to process samples in an automated fashion, and 3) User bias in field selection can undermine the integrity of datasets, especially when manually sampling only small numbers of fields. (more...)

Brachytherapy is an advanced cancer treatment that delivers a targeted high dose rate (HDR) of radiation directly to the tumor. Brachytherapy is a widely used method for the treatment of various cancers, including gynecological and skin cancer. However, success of brachytherapy relies on accurate fit between the applicator and the patient surface. Currently used standard applicators usually fit poorly to the patient, resulting in air gaps that reduce the effectiveness of treatment. The invention herein provides a method to fabricate a mold of a part of the patient's body for the utilization of a brachytherapy applicator to treat various forms of lesions. (more...)

SMAP Site License Agreement for 2010. (more...)

CE-Combinatorial Extension, Algorithms and Computer Programs for Comparing the 3-dimensional Structures of Protein Molecules.   Download Site License. (more...)

Clock networks in high-performance designs are extremely power hungry. Currently there is not a methodology to create resonant clock meshes that resonate at multiple frequencies. Dynamic frequency scaling is common technique to save power in both the clock network and in data-path logic on computer chips. While prior resonant clock networks can save power by recycling energy in the clock network, they do not save any power in the data-path logic. Prior resonant clocks only work at a single resonant frequency (more...)

Modern data centers host many different services or "tenants" on shared network infrastructure. However, determining how to apportion bandwidth across tenants is a fundamental challenge, affecting tenant performance and network operating efficiency. Indeed, there are now many different tenant "isolation models"; each supporting some class of tenants (e.g., big-data processing or low-latency web page construction). Previously, only one isolation model could be used within a data center, forcing network operators into either/or scenarios and limiting their ability to create new models to support emerging services. (more...)

This new method of transcoding can handle memory hardware errors, allowing for aggressive voltage scaling (lowering power use) without sacrificing the quality of streaming data services. (more...)

Improper memory management in software can cause performance to decline and eventual program failure. These problems can be difficult to detect during testing due to the unpredictable amount of time it can take to exhibit overt symptoms, and those symptoms may appear unrelated to memory management.  UCSD inventors have come up with a way to diagnose difficult memory errors that other memory check tools will miss. This invention would be an excellent addition to any integrated development environment for the C++ language. This invention has been used to detect heap growth problems in several widely-used open source software systems such as browsers, a graphics library, and others, and found errors that had been present in shipping product since at least 2007. It can easily be applied to multi-threaded environments. It is especially applicable to mission-critical software. (more...)

UCSD inventors have come up with an automated method to recognize expressions as defined by the Facial Action Coding System of Ekman and Friesen. The technique provides more accurate results than the competition, and is especially adapted for recognizing spontaneous expression. The invention is implemented in a working prototype that can currently work at a real-time frame rate of 6 frames per second.UCSD is currently entertaining an offer for an exclusive license. Should anyone wish to propose their own business plan that requires non-exclusive use of the technology, please send this to invent@ucsd.edu before March 15, 2012. (more...)

There are problems with discrimination speech from background noise in applications such as cell phones, hearing aids, telecommunications, automatic speech recognition, which limit the use of these important technologies. In response to this challenge, investigators at University of California at Berkeley have developed a speech filtering algorithm that improves intelligibility of speech in noisy backgrounds.  This speech filtering algorithm is applied as a first stage of processing, before transmission, analysis, or listening.  The speech filtering algorithm can be located in its entirety on a dedicated DSP or FPGA.   These systems allow the complexity needed for the computations of the gain stage, but still function fast enough for real-time denoising. The investigators have implemented the speech filtering algorithm using a computer to process signals offline (post-hoc). The inspiration for our model comes from our research on the statistics of animal vocalizations (including human speech) and on the responses of auditory neurons to these sounds. They have shown that neurons in avian primary and secondary auditory areas are tuned to represent the statistical structure of vocalizations. These areas are analogous to cortical auditory areas in humans.  The preferred embodiment uses many relatively narrow bands in the analysis filter-as low as 50 Hz bandwidth and spacing. Another embodiment uses fewer, wider bands in the analysis filter, perhaps several thousand Hz in width.The most significant advantage of X is its ability to exploit important, basic statistical information about all human speech in a simple fashion. Some of these properties are included implicitly in advanced ASR systems. Separating these simple, physically-driven features from more complicated verbal and syntactic rules brings this power to bear in simpler, lower-power systems like cell phones. Additional complexity is also the primary drawback of this system: it requires more computational power, and because it uses a longer history, it could introduce delays that are unacceptable for low- like hearing aids and cochlear implants. (more...)

A novel method for making a metal layer semiconductor laser with large bandwidth and the capability for high power output. (more...)

Methods that define the operation of parallel computation for multiple-computer interaction and cloud computing. (more...)

A novel method for visualizing and classifying malware using image processing techniques, applicable to malware detection and anti-virus software. (more...)

Blur and noise are the two common problems that exist in digital imaging. An important camera setting that strongly effects these two distortions, and that needs to be carefully adjusted, is the aperture size. If the exposure time is fixed, a large aperture will increase the signal to noise ratio (SNR), meanwhile reducing the depth of field (DOF) and thus increasing the out-of-focus blur, which eliminates high-frequency components of the image. On the other hand, a small aperture will alleviate the blur but increase the noise level (digital equivalent of film grain). Noise can also be suppressed by using longer exposure time; but of course, this may cause motion blur that is even more difficult to remove. At the same time limited accuracy of auto-focus systems and low light condition may add extra blur and noise into the image. So in real applications, such as consumer digital imaging, it is very common to record weakly blurred and relatively noisy images. (more...)

Although computer-generated (CG) effects enable actors to appear visually realistic in virtual worlds, producing realistic interaction between real actors and virtual objects, features, or characters remains challenging. Because actors often perform outside the context of a virtual scene, seamless integration relies heavily on manual post-processing efforts to synchronize an actor's performance with CG effects.  Prof. Victor Zordan at UCR has developed a technique that previsualizes final integrated scenes at the time of performance acquisition. The technique is able to synthesize realistic dynamic interactions in the virtual world while faithfully preserving the nuances of the actor's performance. The system combines real-time motion capture with physical simulation to generate visible response to virtual interaction while: allowing the actor to respond in a timely manner; curbing the need for the capture of physical artifacts; and creating a host of solutions for hard-to-capture scenarios including custom character-character interactions.  UCR’s technology will find utility in the effects, games, and motion picture industries for generating realistic interaction between characters and objects (or other characters) in their environment. The Office of Technology Commercialization is currently looking for partners who will license this technology from UCR. (more...)

A novel software that automatically and accurately synchronizes pre-segmented transcripts with corresponding videos. (more...)

Researchers at the University of California, Irvine have developed a novel, non-invasive system to measure, quantify and analyze the spontaneous movements of infants in order to predict neurological disorders. The system involves capturing subtle movements of infants. This information is then analyzed and modeled by software. Movements identified may indicate that the infant has an increased risk for cerebral palsy, seizures, autism, intraventricular hemorrhage, cognitive delay or other neurological or motor conditions. By comparing to standards, the information may be used by a clinician to categorize the infant as either a high risk or low risk for the development of a neurological disorder. (more...)

UC San Diego inventors have developed error-correcting codes that allow for double- and triple-error correction. These codes can be applied to communications and memory storage, especially for write-once memory.Additionally, UC San Diego inventors have developed codes for write-once memory that allows for two writes in an efficient manner. This invention can be applied to make more efficient use of flash memory, or other types of write-once memory devices.The research behind these inventions can be reviewed at these links. http://itw2010dublin.org/cs_memories.htm http://www.eurekalert.org/pub_releases/2010-10/uoc--usd102510.php (more...)

The research projects conducted by undergraduate students are frequently driven by the need to fulfill the requirements of specific assignments within the framework of formal course curricular.  It is desirable to have an internet-accessible software tool that supports students to discover and access library and other information resources to complete scholarly research projects related to their coursework. The library information retrieval system is not designed to recommend broad publication databases, rather than specific documents, in response to user queries. However, the undergraduate researchers are often unfamiliar with the expert vocabulary of the subject they are researching or the organization of scholarly literature.  Therefore, it is a challenge for them to effectively retrieve the most relevant scholarly information. (more...)

Magnetoencephalography (MEG) is a functional imaging modality that directly detects neuronal activity with a millisecond temporal resolution. UC San Diego researchers previously developed a multi-core beamformer (MCBF, see SD2010-340) approach that reconstructs common-mode source time-courses and their correlations networks from noisy MEG data, without requiring both a priori information and expensive and impractical computation. However, the performance of MCBF degrades at low correlations and cannot reconstruct individual source time-courses.A detailed description for the related technology SD2010-340 can be found at http://invent.ucsd.edu/technology/cases/2010/SD2010-340.shtml. (more...)

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A novel photography method that provides, along with the actual picture taken, several alternative versions of the image. This method produces photo variations such as panoramas, collages, alternative views, composites based on moving subjects, and views using varying capture parameters such as focal length and exposure time. (more...)

Given here is a novel method to reduce the time-cost of accessing data stored in a computer file system, particularly on a very fast solid-state disk. Normally, to access data in a file system, an application makes a call to the operating system, which invokes the file system to determine where the data resides in the storage device and whether the application has permission to access it. On next generation solid-state drives (SSDs), this is projected to create approximately 7.8 microseconds of latency for each access of the storage device. The approach taken here eliminates nearly all the overhead related to accessing the device aside from the raw hardware cost, reducing latency by 64 percent for 512-byte operations without compromise to system security and access protocols. (more...)

Researchers at UC Berkeley have developed methods and devices for enhancing overall throughput in wireless communication by exploiting the information about the channel gains of the various receiving nodes beyond prediction. This method will provide significant throughput increase even when the delayed channel information is not useful for prediction. (more...)

While teleimmersion has great potential, available algorithms for real-time stereo reconstruction require several seconds to several minutes to process two images and produce accurate stereo output.  Available FPGA and GPU implementations have inherent drawbacks in ability to reconstruct homogenous regions or regions with repeating patterns. The time-of-flight cameras have low resolution, limited range, high noise, and albedo sensitivity. Therefore,  a practical real-time stereo reconstruction is needed for a system enabling geographically distributed users to interact with each other in a shared virtual space.   University of California investigators have responded to this challenge by developing INTI Multiview, a real-time stereo reconstitution integration for 3D telleimmersion.  With INTI Multiview, each user is presented by their 3D avatar generated in real time. INTI Multiview focuses primarily on integrating multiple stereo reconstructions from different views.  Levels of accuracy comparable to other methods are achieved at a much faster speed on CPU by taking a hybrid approach: performing a local optimization technique (the region matching) and using a global optimization approximation to improve the initial results (anisotropic diffusion).  The investigators have implemented a novel multiscale representation that allows for the highly accurate reconstruction of a scene.  The investigators have successfully tested INTI Multiview in many application areas, such as remote dance choreography, shared geoscientific and archeological applications, and training. This work has further extensions in other applications where real-time stereo data is necessary, e.g. full body motion capture, surveillance and tracking, foreground/background segmentation, autonomous vehicle control.  Markerless 3D reconstruction for human movement analysis (motion capture, visual feedback for gaming, rehabilitation etc.)   (more...)

A novel method for measuring the precise visual distortion experienced by an individual MD patient. This measurement is the stepping stone for the development of updateable visual aids. (more...)

Current computing systems typically do not store information about the provenance or origins of the files they contain. More specifically, the information sources used to create the file is also unknown. UCI researchers have developed GARM, a new tool for tracing data provenance and enforcing data access policies with arbitrary binaries. (more...)

Multi-Copy Cache (MC2) is a new cache architecture that enables significant reduction in energy consumption through aggressive voltage scaling, while maintaining high reliability of the cache. This architecture results in a highly energy efficient cache with minimal impact on the area and the access timing of the cache. (more...)

Instant Messaging or “IM” is increasingly used as a communication and awareness tool for work and entertainment. However, this instant awareness is inherently posing risks to one’s privacy. To address this conflict , researchers at UCI’s Department of Informatics have developed PRISM: a plugin that enhances support for privacy management in IM. (more...)

The amount and diversity of patient data available for clinicians is steadily increasing. As a result, patient management for diseases, such as cancer, increasingly involves a multidisciplinary team (MDT) of clinicians from a range of specialties and sometimes from several different institutions. MDTs, such as tumor boards, meet regularly to collectively review clinical data and select treatment plans. To collaborate effectively, clinicians need a way to efficiently assemble a team, convenient meeting place and time, and access relevant patient data. MDT meetings currently take place in either face-to-face, via teleconference, or over the internet (e.g., email and video conference), but these kinds of meetings present number of logistical challenges, especially if clinicians are based at different institutions. For example, it is sometimes difficult for all members of the MDT to be present at a scheduled meeting and/or difficult to assemble all the relevant data for the meeting. Additionally, the decision-making process is not completely recorded because current modes of communication (e.g. email) are not integrated with the EMR. These factors can slow down access to critical patient information and ultimately impair the ability of the MDT to make effective decisions. There is a need for an efficient way to conduct MDT meetings so that all relevant information is accessible from a single, convenient location, with improved annotation of the decision-making process. Description: UCSF inventors have created a web-based software platform that enables MDTs to meet in an online, virtual environment at a time and location convenient for each physician. The platform is designed to be flexible, allowing meetings between groups as small as two conferring over a single patient as well as meetings between large teams conferring over the care of multiple patients. Further, the system is interoperable between institutions and thus allows for efficient collaboration between clinicians from different institutions. The software has an easy to use graphical interface and is fully integrated with the EMR. Physicians can easily import relevant medical reports, digital pathology images and radiographs and describe relevant findings and opinions (using text, voice or video input) in a single, virtual, meeting location. These virtual meetings can be set to automatically to terminate after a period of time, upon which the discussion and consensus patient care plan can be recorded and archived into the EMR. These features enable MDTs to meet conveniently and efficiently discuss patient management decisions. (more...)

In brief, the MRV algorithm developed at UCI speeds certain data processing tasks by a factor of 5 to 10 fold. The fundamental principal behind MRV is that the brute force method need not be performed when the ordering of the dimensions to be reduced satisfied certain conditions and moreover, when datasets do not satisfy these conditions, the MRV transforms the data set so that the algorithm can be applied and speed enhancements can be achieved. (more...)

EdgeCasting is a network architecture and protocol for streaming high quality video to a large population at a low cost. This unique approach offers a high degree of utilization of network resources. (more...)

One of the most serious disadvantages of fully adaptive wormhole routers is its performance degradation due to the routing decision time. The key to overcome this shortcoming is the use of different clocks in a head flit and body flits because the body flits can be forwarded immediately and the FIFO operates faster than route decision logic in an adaptive router. (more...)

Tiled multi-projector displays are becoming increasingly more popular for visualization, education, entertainment, training and simulation applications but registering multiple projectors on such a display presents many challenges. Existing solutions are complex, expensive and often require a highly skilled technician to operate. (more...)

This invention describes a system for collecting, filtering, processing, and ranking information related to user-generated content in 3D virtual worlds such as Second Life® for the purpose of creating a search service for 3D content. (more...)

In multi-camera surveillance, visual tracking, video conferencing and similar applications, the geometric calibration of cameras plays an important role.  Accurate calibration to a global coordinate system is especially important for tracking dynamic targets and 3D reconstruction.  Currently three main approaches are employed for multi-camera calibration: (1) image-based calibration using checkerboards or grids; (2) self-calibration using natural features; and (3) LED-based calibration using one-dimensional objects. The drawback of the first approach is that it is invasive to the environment (e.g. printed targets have to be placed on the floor). The second approach presents difficulties due to variability of natural features in quantity and number.  The third, LED-based approach currently requires all cameras to overlap in a common workspace. Scientists at UC Berkeley developed a novel combinational approach to multi-camera calibration that addresses the diversity of camera placement and requires only a pair-wise workspace overlap between cameras. The calibration process is hierarchical and can be applied to diverse layouts of single cameras, stereo pairs, and camera arrays, including situations where some cameras in the system are facing the opposite directions. (more...)

TCP is one of the core protocols of the Internet protocol suite, and TCP congestion control is one of the most important TCP related requests for comments (RFCs) in recent years. Fairness is an important criterion in congestion control such that two flows competing on the same narrow link node but with different propagation delays should achieve the fair share, but this does not happen with the TCP scheme currently deployed on the Internet. Previous TCP congestion control schemes include FAST TCP, which is round-trip-time fair and scalable, but lacks in friendliness to legacy TCP making it unusable realistically; TCP Hybla which has been successfully deployed on satellite networks but proves to be too aggressive and hence unstable when deployed on the internet; and BIC TCP which improves the fairness of some high-speed schemes, but is not as good as the fairness provided by legacy TCP. Regarding wireless networks, standard cell phones do not have a fast transport layer protocol installed, but rather rely on the old TCP Tahoe implementation at the client side, resulting in a lack of speed in 3G and beyond networks. TCP Libra as a fast transport layer protocol is a solution to improving the speed of cell phone networks. (more...)

There are three approaches for generating frequent itemsets (FI). The first is the candidate set generate-and-test approach. Most previous algorithms belong to this group. The second is a sampling approach. This reduces computation complexity but the result is incomplete. The third is a data transformation approach. The FP-tree method and the pattern decomposition algorithm (PDA) are examples of this approach. They both greatly reduce the original dataset and also do not need to generate candidate sets.Generating FI, however, becomes infeasible if the frequent patterns are long because of the exponential number of frequent itemsets. Algorithms mining frequent closed itemsets (FCI) can have the same problem. Therefore, researchers turn to finding maximal frequent itemsets (MFI). A MFI is a frequent itemset that is not a subset of any other frequent itemset. Given a set of MFI, it is easy to analyze many properties of the dataset. (more...)

The Internet has become a ubiquitous tool in many aspects of society, yet remains surprisingly susceptible to attacks. Even a single malicious node along the pathway from sender to receiver can corrupt communication in a meaningful way. Secure routing protocols attempt to verify that packets of data are correctly delivered to their destination. However, the internet is large, heterogeneous, complex in topology, and dynamically changing. Failure localization and path-quality monitoring in the public key setting have therefore become two of the biggest challenges in communication. Current routing protocols such as link-state and distance-vector are susceptible to loops, slow convergence, oscillations, and suffer from high communication overhead. The number of network applications continues to increase, and the need for secure, dynamic routing that is resilient to malicious adversaries is evident. (more...)

UCLA researchers have developed an adaptive prefetch scheme that may be applied to almost any network application in which files on a remote server may be needed and for which it is possible to estimate the probability of accessing the files. The most obvious example is web browsing. This prefetch scheme has two main components: 1) an adaptive prefetch algorithm, which can be used to obtain files on remote servers before a user requests them, so that the average delay of accessing these files is reduced, and 2) a GUI, which adds icons to each web link on a page that indicate the quality and condition of the link to assist the user in deciding whether to access any particular link. Earlier prefetching schemes simply prefetch a fixed number of pages or pages above a fixed threshold value. These are not adaptive to network conditions, so there is often no real improvement on system performance. This new adaptive prefetch scheme predicts how likely it is that a user will request files based on access history. It determines not only which pages are requested, but also from which page the request is initiated. It also assesses the quality of the link based on the network capacity, system load, and takes into account the cost of bandwidth and usage time. This prefetch scheme can be incorporated into a Web browser, and the techniques may be applied in other caching applications as well. (more...)

UC San Diego researchers have invented powerful software for generating multiple-user, pan-tilt-zoom views from a single commercially available video camera. This invention has advantages over the current art by allowing multiple customized view generation from a single video stream with varying security levels. This method allows for dynamic exploration of remote sites using standard computing platforms. Additional applications of face recognition, infra-red viewing, and general image processing are possible. (more...)

Researchers at the University of California at San Diego have developed a method that finds the simplest characterization of complex algebraic systems, particularly ones that contain variables subject to random statistical fluctuations. For example, an NxN correlation matrix contains N(N+1)/2 elements (taking symmetry into account), but they are usually not independent of each other and, in addition, they are subject to random sampling fluctuations. The standard method of estimating the correlation matrix assumes that its elements are independent and ignores the statistical fluctuations. It therefore interprets sampling fluctuations as real correlations. This undermines our ability to use the estimated correlation matrix to predict the correlations expected in other samples. The problem is further exacerbated if the input data is incomplete, in which case the standard estimate of the correlation matrix might not even satisfy basic mathematical requirements, for example that it be positive definite. The Algebron method seeks to characterize the system with the minimal number of parameters required to fit the data. It takes into account the statistical fluctuations in the data and any incomplete sampling. The derived parameters are the most reliable that can be determined from the data and provide the best prediction for the behavior of other samples. Commercial applications would use the robustness and predictive power of correlation matrices determined with the Algebron method. There are many potential fields of use: e.g., risk analysis, financial forecasting, and marketing and inventory control. (more...)

A new audio coding method was developed that allows efficient decomposition of audio signal into periodic and noise components. The components can be recombined after processing operations, such as compression or editing, to reconstruct a modified version of the audio signal. The sound model can be used also to store and modify clips of sounds for synthesis applications, such as concatenative synthesis of speech or music. (more...)

UC San Diego inventors at the San Diego Supercomputer Center have invented a new, more powerful method of managing data. This technology removes the need for a data intermediary, required of the current generation of so-called federated databases. By creating on-the-fly a knowledge base from disparate data systems, the end user can have more power to add and remove data sources. A working prototype is ready for demonstration. (more...)

UC San Diego researchers have invented a way to reduce cabling complexities in large networks (especially those commonly used in large data centers). The core of the switching infrastructure is scalable and capable of switching 10's of terabits/sec of network bandwidth, all without involving any backplane. The design involves hardware to minimize cable crossover and a custom protocol that reduces cables by a factor of 500 and adds less than 300 nanoseconds of latency. The concept for a design of a 27,648-port gigabit Ethernet switch is complete and a hardware prototype demonstrating the technology is under construction. (more...)

Aerial spin labeling (ASL) is a powerful MRI technique for non-invasive perfusion imaging of the brain and other organs using arterial blood water as the endogenous contrast agent. However, the conventional spatially and non-vessel selective ASL methods are problematic in that the life of the tracer is shorter than the time of delivery of the tagged blood to the target tissue. The delivery time arises from variations in the distances and flow velocities along the vascular tree from the tagging location to the tissues of interest. The deliver time to the target tissue in pathological cases can be much longer then in healthy subjects. In the important application of stroke, this can lead to false positive findings of low perfusion when, in fact, perfusion is present via collateral routes of circulation. (more...)

Simgrid is a toolkit that provides core functionalities for the simulation of distributed applications in heterogeneous distributed environments. The specific goal of the project is to facilitate research in the are of distributed and parallel application scheduling on distributed computing platforms ranging from simple network of workstations to Computational Grids. (more...)

bmpcount implements a family of bitmap algorithms that count active flows at high speeds. Due to its modular structure it can be adapted to any instance of the isomorphic problem of counting the number of distinct elements in a multiset, with small per-element processing. Various members of the family are specialized to take advantage of specific particularities of the application: virtual bitmap is suited when the accuracy of counts is important only in a narrow range (e.g. triggers), multi resolution bitmap when it is important over a wide range and adaptive bitmap when repeated measurements are expected to give similar counts. (more...)

Programmers at UCSD's California Institute for Telecommunications and Information Technology (CAL-IT(2)) have developed a traveler information system that offers personalized traffic updates through your cell phone.   This technology is also described at the following web links   http://www.calit2.net/briefingPapers/sdTraffic.html http://traffic.calit2.net (more...)

University inventors have solved the problem of how to rapidly memorize a map. One promising application would be as software sold bundled with map data in order to review and study maps more effectively. The technology can be applied to tools for memorization-intensive vocations, such as the military, transportation, and delivery. (more...)

The invention allows for the determination of amino acid sequence tags from tandem mass spectrometry spectral pairs and subsequent peptide and modification identification through a database search utilizing extremely fast pattern matching. This invention would present an improved method over tools, such as SEQUEST and MASCOT, by never comparing a spectrum against a database and simultaneously allowing for higher sensitivity in the detection of post-translational modifications. The invention is useful to anyone interested in identifying peptides, proteins and post-translational modifications on Tandem Mass Spectrometry data from biological samples (more...)

Inventors at UCSD have discovered a new and robust method for detecting objects in images, video streams, or signal streams. Many current object recognition methods require numerous training examples to be used to improve system performance. The current method does not have such training size limitations and can thus also be used for the design of real-time object/signal detectors in applications with limited training size availability (more...)

UC San Diego inventors have come up with a way to efficiently parallelize linear programming solvers using a fast-converging iterative method. The invention compares favorably against traditional conjugate-gradient methods (which are difficult to parallelize) and traditional iterative solvers (which are slow to converge to a solution). The method enables improved performance for the following industrial applications: Business Administration Product mix planningDistribution networksTruck routingStaff schedulingFinancial portfolios optimizationProfit maximizationCorporate restructuring Telecommunications Call routingNetwork designDecoding error-correcting codesInternet trafficNon-linear sampling (compressed sensing) Transportation Vehicle/packages routing (FedEx, UPS) Manufacturing VLSI chip board manufacturing Machine LearningSocial NetworksStatistical Software Packages (more...)

Background: Cigarette smoking is the single most preventable cause of premature death in the United States. Each year, one in every five deaths, (about 443,000 in total) is smoking related. The health risks associated with smoking translate into annual healthcare costs of more than $96 billion, with costs associated with second hand smoking averaging $10 billion. Interestingly, 70% of the 43.4 million U.S. adult smokers report that they want to quit completely and more than 40% try to quit each year. However, smoking cessation is extremely difficult; in fact, only about 4% - 7% of people are able to remain smoke free for six months on any given attempt. These success rates dramatically increase to between 14% - 27% if smokers use medicines or behavioral therapies, but such methods may be expensive for both the insurer and patient, inconvenient, or difficult to access. Therefore, it is imperative that a successful, convenient, and cost-effective smoking cessation aid be developed. Invention: Prominent University of California clinicians, Ricardo F. Muñoz, Ph.D. and Eliseo J. Pérez-Stable, M.D. have developed an extremely successful, web-based, smoking cessation program. The program takes eight weeks to complete and combines a smoking cessation guide with individually tailored advice, optional email reminders, and an optional mood management program. Since 2002, over 17,500 smokers from over 155 countries have participated in a series of randomized controlled smoking cessation trials using this program. The study boasts an impressive success rate, with 20% of the participants remaining smoke-free after one year. Significantly, this success rate is comparable to those seen for nicotine replacement therapies, or smoking cessation groups, yet the web program has the important advantages of reducing the cost per patient and increasing the ease of patient access. Furthermore, this fully developed stand alone program is available in both English and Spanish, making it accessible to virtually every American smoker. http://www.stopsmoking.ucsf.edu or http://www.dejardefumar.ucsf.edu (more...)

COPYRIGHT (C) 1978, 1979 REGENTS OF THE UNIVERSITY OF CALIFORNIA All Rights Reserved UCSD Pascal versions authored solely by UC authors prior to June 1, 1979 may be licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License (http://creativecommons.org/licenses/by-nc-sa/3.0/legalcode) or the following. Permission to use, copy, modify, and distribute any part of UCSD PASCAL solely authored by UC authors before June 1, 1979 for educational, research, and non-profit purposes, without fee, and without a written agreement is hereby granted, provided that the above copyright notice, this paragraph and the following three paragraphs appear in all copies. Those desiring to incorporate UCSD PASCAL into commercial products or use for commercial purposes should contact the Technology Transfer Office, University of California, San Diego, 9500 Gilman Drive, Mail Code 0910, La Jolla, CA 92093-0910, Ph: (858) 534-5815, FAX: (858) 534-7345, E-mail: invent@ucsd.edu. IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF UCSD PASCAL, EVEN IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. THE SOFTWARE PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. THE UNIVERSITY OF CALIFORNIA MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER IMPLIED OR EXPRESS, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF UCSD PASCAL WILL NOT INFRINGE ANY PATENT, TRADEMARK, OR OTHER RIGHTS. Version I.5 (zip file) Version I.4 (coming soon) (more...)

The U.S. National Health Interview Survey (HHIS) Public Use Data files cover topics similar to some of those employed by the Quality of Well-Being Scale (QWB) instrument. The QWB develops a single, overall expression of Well-being on a scale running from 0.0 (for death) to 1.0 (for asymptomatic full function). The NHIS Public Use Data, however, produces no single overall score, but frequencies in each of several different categories of dysfunction. The Quality of Well-Being Scale, Extended #1 (QWBXI) provides a single estimated QWB-like score for each individual in the NHIS survey, derived from the NHIS data. The QWBX1 score might be used, after matching by case ID# with other NHIS data files, to estimate the burden of particular diseases or conditions on the U.S. population. Other uses are quite possible. Estimated QWBX1 scores have currently been generated for the years 1982-1994 and are available by individual year or groups of years. (more...)

Family Pairwise Search (FPS) is a method for scoring a single biological sequence against a family of sequences. FPS compares pairs of sequences and then combines the pairwise scores into an overall score for the match of the single sequence to the family of sequences. FPS operates in two modes. In the single-sequence mode, FPS compares a single query sequence to a library of sequence families. The query consists of a single sequence, and the target library consists of families of sequences. The result is a family classification for the query sequence. In family-query mode, FPS compares a query set of related sequences to a database of single sequences. In this mode, FPS outputs a set of sequences from the database that are related to the query family. Further technical information on FPS may be found at the San Diego Supercomputer Center website address, fps.sdsc.edu. (more...)

The equalizer is a custom application that uses rank-order similarity in gene expression intensity to construct non-linear equalization vectors that are then used to linerize the data matrix to a consistent slope of 1. In addition, the equalizer rationally eliminates "negative" values of expression seen in Affymetrix data. Use of the equalizer greatly facilitates downstream data analysis. This software has been used for Affymetrix chip analysis but has applications to other microarray systems as well. See also: Robert O. Stuart, Kevin T. Bush, and Sanjay K. Nigam. 2001. Changes in Global Gene Expression Patterns During Development and Maturation of the Rat Kidney. PNAS. 98:5649-54). (more...)

University researchers have written an instruction-level simulator of a simultaneous multi-threading (also known as hyper-threading) processor. The software provides detailed simulations of a pipelined out of order processor with all sources of latency modeled. The software is compatible with Unix operating systems using a standard C compiler. A minimum of 64 Megabytes of RAM storage are recommended, along with a printer for reporting out results. Source code is available. (more...)

Researchers at UCSD have produced bioinformatics middleware for working with protein and nucleic acid macromolecular structure data stored in the new standard mmCIF format now being supported by the Protein Data Bank. The software will be very useful to researchers in basic and applied research in biology, biochemistry, pharmacology, medical research, molecular biology and protein chemistry. The toolkit contains software for parsing mmCIF files, loading the molecular structure data into a relational database, translating the data into XML formatted files, and running an OMG standard LSR/MMS CORBA server. The software is written entirely in Java. (more...)

University researchers have written powerful software for the molecular modeling of protein. The Fast Atomic Density Evaluation (FADE) and Pairwise Atomic Density Reverse Engineering (PADRE) programs deduce molecular shape using the local density of atoms at points within a few Angstroms of the molecular surface. FADE uses Fast Fourier Transforms and convolution integrals to rapidly calculate the distribution of atomic neighbors. PADRE poses the question of atomic density as an inverse problem based on a one-dimensional integral of Lennard-Jones potentials. A primary advantage of atomic density methods is their computational efficiency. FADE can analyze molecular shape in seconds, while other methods may take minutes or hours. FADE and PADRE can deduce surface shape features, such as crevices and protrusions. FADE is also able to do detailed analysis of shape complementarity for docked complexes. The ability to determine regions of strong shape match or mismatch in an interface is very useful to computer-aided drug design. In addition to research, atomic density methods offer an ideal tool for learning about the shape features of molecules. The basic ideas underlying density methods can be understood intuitively, and integration within existing packages for molecular visualization would be a great aid to students studying protein structure-function relationships. For more information please see the website http://www.sdsc.edu/CCMS/FP/ (more...)

GenePalette is a powerful cross-platform and cross-species bioinformatics tool for genome sequence visualization and navigation. Written in Java, this program allows users on Mac, PC, or UNIX platforms to access genome sequence data quickly and easily through a unified interface. Users can download from NCBI's GenBank database large or small segments of genome sequence from a variety of organisms (e.g., yeast, human, fly, worm, mouse, plants), preserving the gene annotation that is associated with that sequence. Sequence elements of interest (transcription factor binding sites and other regulatory motifs, restriction enzyme sites, primer sequences, SNPs, microsatellites, etc.) can be searched for and identified in the loaded sequence, and then clearly visualized within a colorful graphical representation of gene organization and intron/exon structure. Among the many features that GenePalette provides are intuitive clickable user interface elements; customizable libraries of user-defined sequence features; the ability to export both graphical and nucleotide views of genomic sequence data in GIF format; and a restriction enzyme site library containing more than 200 sites. See http://www.genepalette.org (more...)

This invention allows desktop and laptop computers that are idle and connected over a wired network to be turned off—or put into a low-power mode, such as sleep (called S3 in Windows/ACPI)—and later woken up transparently when a user-specified event occurs. This event can be anything, such as a remote login request (remote desktop, SSH, file access), etc. The computers under sleep maintain their accessibility (ICMP ping responses, answer ARP requests, maintain DHCP leases) even though they are in a low-power mode. Since the computers are effectively in a low-power state and can be woken up “on demand,” the energy savings are substantial. The scheme does not require any changes to the routers, switches, or any of the hardware additions to the desktop computers themselves that want to use the scheme and only needs software on the computers that want to use it, as well as the addition of a “sleep-server.” (more...)

A search engine has been developed that interfaces with PubMed enabling a search of the published biomedical literature to identify researchers and/or faculty of a named research institution who have published in a specific user-defined research area. The search engine is currently designed to search for UCSD-affiliated researchers, but the parameters in the algorithms could easily be modified to specifically identify researchers at any given research establishment. The primary advantage of this search engine is obvious: to promote research collaborations, cooperation,  teamwork, and synergy within a large university or research establishment, such as a multi-national corporation. The authors do not have to continually update their publication list, as this is done through the PubMed database. A Site Use License is available: Search Engine License (more...)

This is a browser-based software system that was designed by, and for use in, emergency medicine departments. The system provides electronic documentation capabilities for maintaining up-to-date information on all patients seen and treated in the emergency department. (more...)

HDDErase.exe is a DOS based command-line utility to securely erase all data on ATA disk drives in Intel architecture computers. Download the commercial license at: Copyright License Agreement (more...)

Health care in the United States is based on a reimbursement system; all medical staff are required to bill for various medical treatments and the health care provider is reimbursed by a payer—such as a private insurance company or government health care fund. The reimbursements are based on specific billing codes and the claims initiated and submitted by the health care provider. The environment, however, is rapidly changing and becoming extremely complex, such that billing codes and code edits change quarterly. Understanding the meaning of the billing codes and applying them properly for the services provided to patients is challenging. As a result, many clinics and/or hospital facilities end up either over charging or under charging insurance, or there is missing documentation requiring additional communication between hospital and payee, or missed charges. One study reported that radiation oncology billing error rates ranged annually from 11 percent to 37 percent, corresponding to $7M to $25M for a medium sized clinic. (more...)

To date, no methods have been very successful in determining fine structural details of specific complex objects. Although imaging tools such as electron microscope tomography allow 1nm resolution in biological systems, there is generally a lot of associated background noise due to nonspecific staining. Methods of analyzing tomography images such as Fourier, correlation, and model fitting fail to filter through the low signal to noise ratios since they provide information on global frequency content, but no information on where particular frequencies occur. UCSF investigators have developed a new wavelet-based image processing algorithm that can determine where particular frequencies occur, independent of how often they occur. (more...)

BACKGROUND: Flow cytometry and cell sorting are well-established technologies that allow for rapid multiparametric analysis of cells on an individual basis, and also for separation of highly purified populations of cells. Because the technology collects quantitative data regarding cellular size, granularity, and fluorescence intensity signals, it has found many basic research, clinical, and industrial applications. Researchers demands for more intricate, high-throughput analyses have led to modern machines that simultaneously measure many phenotypic and functional parameters, while functioning at high speeds. Future studies will require flow cytometers to deliver increasingly precise data and better detection of rare events.Along with demands for better, more sophisticated instruments, there is also great need for less expensive, simpler machines. The vast majority of flow cytometers are used in clinical diagnostics, where the drive for better and more practical tests imposes demands for inexpensive and robust analysis. Additionally, typical machines are prohibitively expensive for many resource-poor areas in which monitoring of disease and efficacy of therapies is critical, such as in the detection and monitoring of HIV infection and its progression to AIDS. Though flow cytometers are already used in many diverse areas, as they become cheaper, more manageable, and easier to operate they may become more widespread in immunological and infectious screening, field clinics, water monitoring, agriculture and veterinary diagnostics, and rapidly deployable biothreat detection. INVENTION DESCRIPTION AND ADVANTAGES: UCSF inventors have developed a new flow cytometer design that allows for the manufacture of less expensive hardware, with data quality equal or superior to that of currently available machines. The invention portfolio consists of a new hardware design (SF2008-099) and a generally applicable software analysis package (SF2008-100) for use with either the new hardware design or traditional machines.The new hardware design is technically superior to existing designs because it uses fewer hardware resources but allows collection of a larger amount of information about each particle. When combined with the software analysis package, the information collected can be processed to yield data that are superior to those collected by existing machines. Due to reduced hardware requirements, instruments based on this design will be less costly to manufacture and more reliable than currently-available instruments. Despite these cost savings, the data collected are of equivalent or better quality than those provided by traditional designs. For example, early prototypes show improved resolution of low-intensity signals due to a substantial (9-fold) reduction in the spillover between fluorophores. A licensee of both the hardware and software inventions will be able to manufacture better performing, more reliable flow cytometers and cell sorters for less cost than current designs.The analysis softwarewhich is also available separatelysubstantially improves the sensitivity of flow cytometry to low-intensity signals by reducing errors associated with the conventional compensation process. Analyzing the data from a state-of-the-art, commercially available machine with the new software analysis package instead of currently available packages shows an over 100-fold increase in sensitivity. Additionally, the software package allows for the evaluation of fluorescence spectra to determine optimal filter sets, making the machine easier to operate and configure. A licensee of the software package alone would be able to offer software for analysis of flow cytometry data that provides more sensitive and more correct results than other software. With access to both this invention and the new hardware design, a licensee could offer superior flow cytometers as well as the software necessary to optimally configure the machine and interpret the resulting data. (more...)

Several schemes have been implemented in distributed computer systems which recover execution of program modules when hardware and software failures occur. The distributed recovery block scheme executes a primary and backup copy of a program on multiple processors. The processors communicate to determine which version failed such that the successful processor passes its result on to the next stage. Unfortunately, if one version crashes (fails to execute) the recovery time is prolonged. Additionally, the scheme is expensive to construct for processing more than two versions of a program. Another scheme, the autonomous decentralized software structure, executes more than two versions of the same program but is tolerant for hardware faults only. (more...)

Diabetes is a condition that affects blood vessels throughout the body, particularly in the kidneys and eyes. Diabetic retinopathy is a complication of diabetes and is the leading cause of new blindness in the United States. Diabetic retinopathy results when diabetes affects vessels in the eyes, producing abnormalities such as microaneurysms and hemorrhages. These abnormalities are the same color as that of blood vessels, causing some areas of the normal blood vessel system in the retina to be erroneously classified as defects. Automated systems for detecting diabetic retinopathy have been plagued by high false alarm rates. Performance reported from prior systems using a matched filter response was below the level of a human operator. (more...)

A decade after Java arrived, there have been improvements in the runtime performance of platform-independent virtual-machine based software. However, using such machine-independent software on resource-constrained devices such as mobile phones and PDAs remains a challenge, as both interpretation and just-in-time compilation of the intermediate VM language run into technological limitations. Running VM based code strictly in interpreted mode has severe performance overheads, and as a result requires the device's processor to run at a higher clock speed than if native code were run instead. This leads to an increased power consumption, reduced battery autonomy, and may require the overall use of more expensive processors vs. a pure native-code solution. Just-in-time compilation produces more efficient native code, but the process of getting to that native code may be very costly for our current resource-constrained embedded devices.Consequently, distinct embedded just-in-time compilers have emerged, in which trade-offs are made between resource consumption of the just-in-time compiler and the ultimate execution performance of the code being run on top of the VM. Embedded just-in-time compilers achieve their results using significantly fewer resources than their larger counterparts by using simpler algorithms. One example is the use of linear-scan register allocation instead of a graph-coloring approach, which not only reduces the run-time of the algorithm, but also greatly diminishes the memory footprint. Embedded just-in-time compilers also tend to use less ambitious data structures than "unconstrained" compilers-for example, while the use of Static Single Assignment (SSA) form is fairly standard in large just-in-time compilers running on server-class machines, the time and memory needed to convert the 10% most frequently executed methods to SSA using traditional techniques exceeds the resources of most embedded computers. (more...)

SPI is one of the most popular bus interfaces between a microcontroller and a peripheral device. However, system designers often overlook a bottleneck, which uses SPI inefficiently when transferring between two slave devices. Our technique eliminates this bottleneck with very simple hardware, and this should be of interest to manufacturers of microcontrollers. Peripheral devices would not require any modifications and can be used just as before. (more...)

Researchers at the University of California at Berkeley have identified a plant resistance gene family, the members of which encode plant resistance polypeptides having P-Loop and LRR structural motifs. This resistance gene class includes Prf, RPS2, RPM1, N, and L6 and represents a large fraction of known plant disease resistance genes. The invention further involves transgenic plants and transformed host cells that express these DNAs and exhibit enhanced disease resistance to plant pathogens. For example, when expressed in transgenic plants, Prf confers Fenthion sensitivity and resistance to a wide variety of phytopathogens, including not only Pseudomonas syringae, but also unrelated pathogens such as Xanthomonas campestris. (more...)

The advent of AC current proximity sensors that are passive, wireless, low-costs, and easy to install as well as maintain, enables numerous new energy management application. To take advantage of this technology-enabling opportunity, researchers at UC Berkeley have applied the latest MEMS AC sensor technology to circuit breakers. In this application, the current sensors can be easily attached to the fronts of the breakers installed in breaker boxes – these boxes are common in residential, office and commercial buildings. This type of installation doesn’t require exposure to hazardous wiring, and therefore a professional (expensive) electrician isn’t required for the installation. (more...)

Get Feedback from Completed Projects Occupant surveys are an invaluable source of information for improving the performance of buildings. Surveys allow you to objectively gauge which building services and design features are working and which aren't, and to prioritize the steps needed to improve occupant satisfaction and workplace productivity. Easy and Powerful The Center for the Built Environment (CBE) has developed a cost-effective web-based survey that takes approximately ten minutes to complete. The survey is intuitive and streamlined, it preserves the confidentiality of respondents, and controls access in order to maintain data integrity. Improved Decision Making As soon as the survey is completed, reports are immediately available via a password protected website, and they can be printed directly or downloaded into other documents. These easy-to-understand reports will help you: Evaluate the effectiveness of building service providers Justify facility expenditures to management Assess the effectiveness of improvements Stay aware of the occupants' perceptions of the building Enhance communication between corporate real estate, facility operators, and building occupants Get a LEED Credit The survey's thermal comfort section provides the information you will need to get credit 7.2—thermal comfort verification—with LEED-NC version 2.2. For more information about using the survey for this LEED credit, please see our survey users page. Core Question Areas The standard survey includes questions on the following key aspects of the indoor environment: Office Layout Office Furnishings Thermal Comfort Air Quality Lighting Acoustic Quality Cleanliness and Maintenance General Comments Optional Survey Areas Available CBE has developed additional question sets to gather information on specific aspects of the workplace environment. When needed, CBE can develop modules to investigate new topics. The modules currently available include: Accessibility Building and Grounds Maintenance Service Commute Conference and Training Rooms Court Work Daylighting Laboratories Office Support Equipment Operable Windows Raised Floor and Floor Diffusers Restrooms Safety and Security Wayfinding Take a Demo To see the entire core survey, open the Occupant IEQ Survey Demo. You may also preview a sample of the IEQ Reporting Tool. To learn about the development of the survey tools, go to the survey research page Operation and Maintenance (OM) Survey To complement our occupant survey, CBE has developed a prototype survey designed to gather information on building performance from the perspective of operations and maintenance staff. To take a demo of the OM Survey, click here. Contact Us for More Information These survey resources are available for CBE industry partners, and to the building industry at large. For a list of survey implementation costs, please click here (PDF 125K). For more information, please send us an email or call us at (510) 642-4950.       Occupant Indoor Environmental Quality (IEQ) SurveyTM http://www.cbe.berkeley.edu/research/survey.htm (more...)

In developing regions, computers are often shared among large groups of users, rather than the traditional one-to-one model of usage. This has particularly been observed in the classroom setting, where computers are becoming more common. In response, Single Display Groupware (SDG) has been shown to have great utility in these regions. SDG amortizes the cost of the hardware over all of the users, decreasing the per-user cost. It also allows the hardware purchases to scale more easily as new users are introduced. One system that has utilized this model is Microsoft's Multimouse. Multimouse is an SDG software solution focused on using multiple USB mice to engage groups of students using educational applications. However, as is common with most SDG development interfaces, these applications must be custom-built to utilize the Multimouse technology. Legacy applications are limited to using multiple inputs in a naive way: all mouse actions are assumed to be from the primary mouse. This limits the adoption of Multimouse and other SDG software, as few compatible applications have been developed. There has been a dearth of work on utilizing SDG with legacy educational software. Most of the development in this area deals with integrating with the existing windowing system, not how to correctly operate legacy applications in a SDG environment. Researchers at the University of California, Berkeley have developed algorithms and software which allowing for functional and intuitive use of legacy applications in SDG environments. This innovation provides multi-user interface to legacy software. The UCB research effort is initially focused on education, providing an intuitive user interface for point-and-click educational applications. Because collaboration has been shown to be an important factor in the effectiveness of SDG educational software Metamouse is designed to enforce collaborative behavior among users. See Paper: Metamouse (more...)

UC Berkeley researchers have previously presented a unique label-free method to detect biomolecular binding based on impedance changes using microparticles or nanoparticles in microfluidic channels. This method requires no florescent labeling of analyte and allows a simple readout at a given frequency. This demonstrated microfluidic integration of the nanocavity system is also advantageous, allowing easy introduction of analyte solution and measurement buffer. Because the detection technique is essentially label-free and just depends on the specific binding of anibody-antigen, DNA-DNA, DNA-RNA, DNA-protein, antibody-small molecule, or antibody-cell, this invention could be used to diagnose virtually any disease. Researchers at UC Berkeley have expanded upon this innovation to demonstrate the ability to sequentially load different sized and different types of beads into a microfluidic channel. This has numerous applications, including the ability to successively capture smaller and smaller beads that otherwise would be impossible to capture. In addition, the cells can be mechanically lysed. (more...)

Subject-accrual rate and cost per subject are key factors in any successful research program. Researchers at UC Berkeley have developed a recruitment & data management system which allows users to efficiently trim human subject enrollment timelines and tailor study subject pools to optimally match research requirements. This streamlined system enables easy, effective management of multi-study human subjects program with the added benefit of addressing the legal and ethical challenges of undue inducement commonly faced by researchers. This unique and powerful system has already been successfully utilized by dozens of world-class researchers throughout UC Berkeley. It merges a simple, easy to use interface with powerful proven statistical methods and demographic data resources that can effectively optimize research study pools to best match target populations. This means radically reduced costs per subject; better, more reliable data; and faster time to market.http://sfbay.alkami.org/   (more...)

Human faces are arguably the most extensively studied object in computer-based recognition -- due in part to the many important applications in this field as well as the realization that challenges associated with face recognition are representative of challenges in generalized object recognition. A central issue in research of object recognition systems is the question of which features of an object are most important for recognition. The dominant approaches are based techniques such as Eigenfaces, Fisherfaces, LaplacianFaces, and variants. However, with so many proposed features, there is a lack of guidelines for practitioners, and to-date, face recognition methods cannot achieve satisfactory results compared to human performance. To address these challenges, researchers at UC Berkeley have examined this topic from the new context of the role of feature selection in face recognition from the perspective of sparse representation. This approach has led to an image-based recognition system that outperforms state-of-the-art alternatives. In testing, this approach achieve 96.5% recognition rate using 120 Eigenfaces on the entire Extended Yale B database. Other unconventional features such as severely down-sampled images and completely random projections performed equally well. For example, the holistic features given by images down-sampled to just 12 x 10 pixels achieved 92.4% recognition rate on the same database. (more...)

Controlling electricity utilization on utility grids is a major opportunity for reducing energy usage across large regions. This control is especially valuable when used to minimize peak energy demand. Air conditioning cooling systems in residential, retail and commercial facilities are a large source of peak energy usage, and therefore intelligently monitoring and controlling these AC systems would enable utilities and their customers to better manage energy demand during peak energy periods. To address this opportunity, researchers at UC Berkeley have developed software that enables AC thermostats to be intelligently managed by utilities and customers. This software allows thermostats to be controlled over a network and programmed to operate based the amount of energy demanded from the utility grid. (more...)

Microelectrical mechanical systems (MEMS) are finding applications in a growing variety of fields that in aggregate are emerging as a large MEMS industry. However, despite the huge economic potential of MEMS, the current computer-aided design (CAD) tools for developing these complex devices are rudimentary. To address this situation, researchers at UC Berkeley have developed a MEMS CAD tool that combines evolutionary multi-objective optimization (EMO) with interactive evolutionary computation (IEC). The resulting hybrid solution enables complex MEMS to be designed with target specifications that are optimized for design constraints and competing performance goals. While other MEMS tools that use IEC have been developed, those tools are focused on mask layout, as well as fabrication and parametric modeling. In contrast, the Berkeley hybrid tool is focused on design synthesis. Furthermore, other CAD tools that use EMO depend on simulation software to evaluate design quality -- but many MEMS design issues can't be currently modeled and detected using simulations. However, these design issues can be readily identified by human visual inspection. By taking advantage of this human ability to perceive design flaws that can't be identified by software, this combined IEC - EMO approach produces superior designs with fewer manufacturing problems. (more...)

Advancements in game theory and auction analysis have led to the development of various mechanisms to facilitate exchanging goods, services, and other things of value. For example, the well-known Vickrey-Clarke-Groves (VCG) auctions have beenproposed for various exchange-type applications. Unfortunately, implementations of VCG auctions are often undesirably computationally complex and may require periodic infusions of capital for sustained operability. Such auctions are considered not budget balanced if additional infusions of capital are required. Furthermore, certain applications may require that certain desirable auction properties, such as efficiency, be compromised. An efficient auction may be an auction that maximizes the aggregate benefit to participants, i.e., the social welfare,when participants act to benefit themselves, i.e., they bid selfishly. In addition, conventional auction systems and methods often lack capabilities required for various real-world applications, especially applications involving exchange of combinations of items or things, such as portions of sub-links comprising a communication link. To solve this problem, researchers at UC Berkeley have developed a double-sided exchange wherein both buyers and sellers provide bids for matching via the exchange. A first interface receives buy bids from buyers and a second interface receives sell bids from sellers. A controller matches the sell bids with the buy bids, yielding matched buy bids and matched sell bids in response thereto so that allocations of the matched buy bids and the matched sell bids maximize a surplus of the exchange. An allocation that substantially maximizes an auctioneer's profit and/or announces payments based on sell bids is provided. The announced allocations and prices can be shown to be a substantially competitive equilibrium in some applications.    (more...)

Wireless sensor networks are an emerging research area with potential applications in a wide variety of fields. A primary impediment to the commercial adoption of these networks is that the radio in each wireless sensor node requires lots of power -- especially in comparison to comparable wired sensor nodes. This high power requirement consequently limits the range and/or economics of deploying and maintaining these wireless networks. To solve this problem, researchers at the University of California, Berkeley have developed an innovative media access protocol for wireless sensor networks. This protocol has been developed for sensor networks in which the sensor nodes periodically generate data and have limited power, but the network's main access point is not power constrained. In comparison to protocols designed for more general contention-based (random access) networks, this new protocol lowers power consumption by minimizing the power wasted due to radio operation inefficiencies at each node, and thereby increases battery lifetime. Moreover, this novel protocol offers superior real-time delay guarantees, congestion control and data transmission fairness. In modeling this protocol on a wireless sensor network for traffic management, the results showed that power consumption was 1,000 times lower than the power consumed by a similarly configured contention network protocol -- making the sensor network technology economically viable. (more...)

The technical requirements for transmitting multimedia data in mobile wireless applications (e.g., cellular, 802.11 and video sensor networks) are significantly different from the requirements in wired PC and broadcast TV applications. For example, in contrast to wired and broadcast applications, mobile wireless applications are typically comprised of low-power devices with limited battery charge times, and low-bandwidth networks that are prone to channel loss. Consequently, popular CODECs such as MPEG and H.263 that were developed for wired and broadcast applications fail to simultaneously address the requirements of mobile wireless applications. To address these more demanding requirements, researchers at the University of California at Berkeley have developed a multimedia CODEC and architecture that are optimized for mobile wireless applications. Based on the principles of distributed compression, this Berkeley model represents a significant departure from traditional CODEC models. For mobile wireless multimedia transmission, the Berkeley model has several advantages over existing models. First, in comparison to intra-frame video coding methods, the Berkeley CODEC places low computational complexity on both encoding and decoding. Second, in comparison to full-motion video coding methods, the Berkeley CODEC offers high compression efficiency and can robustly handle packet and even frame drops. And third, in comparison to other distributed CODEC methods, the Berkeley CODEC does not require network feedback. Moreover, the syntax of the Berkeley encoder is rich enough to be easily trans-coded into the bit-streams of popular encoders such as MPEG. (more...)

Hidden Markov Models (HMMs) have been successfully applied to a variety of problems in molecular biology ranging from alignment problems to gene finding and annotation. Alignment problems can be solved with pair HMMs, while gene finding programs rely on generalized HMMs in order to model exon lengths. Researchers at the University of California, Berkeley have developed generalized pair HMMs, an extension of both pair and generalized HMMs. The researchers have demonstrated how generalized pair HMMs, in conjunction with approximate alignments, can be used for cross-species gene finding and can be applied to DNA-cDNA and DNA-protein alignment problems. (more...)

The invention provides methods and compositions for normalizing and amplifying RNA populations. The methods generally comprise the steps OF : (a) copying MRNA to form first ss-cDNA; (b) converting the first ss-cDNA to first ds-cDNA; (C) linearly amplifying the first ds-cDNA to form first ARNA ; (d) tagging the 3'end of the first ARNA with a known sequence to form 3'-tagged first ARNA ; (e) copying the 3'-tagged first ARNA to form second ss-cDNA; and (F) normalizing the MRNA AND/OR the first aRNA. Note that the normalizing step (f), may be implemented prior to step (a), prior to step (d), or prior to both. The invention also provides kits for practicing the subject methods and protocols. These generally comprise one or more reagents used in the methods and instructions describing protocols embodying the subject methods. In a particular embodiment, the kits include premeasured portions of oligo dT T7 biotinylated primer, T7 RNA polymerase, annealed biotinylated primers (used to make Driver pool #1, see Fig. 3), streptavidin beads, polyadenyl transferase, reverse transcriptase, RNase H, DNA pol I, buffers and nucleotides (more...)

Mutation-based validation paradigm (MVP), which is a circuit validation tool for high-level hardware descriptions (more...)

BACKGROUND: Genetic engineering of bacteria has become a prevalent way of producing chemicals, providing a cost-effective, scalable, and environmentally safe manufacturing process. However, maximizing the final product titer remains a challenge, requiring the optimization of the bacteria’s metabolism and the identification of the optimal protein production rates. Currently, the production rates of these proteins are determined through trial and error, by random mutagenesis, or equivalent random selection methods. As such, the development costs are typically very high.   TECHNOLOGY:   UCSF researchers have developed a novel methodology that allows the user to select the production rate of a given protein from very low to very high rates (1 to 100000), thus eliminating the use of trial and error techniques during the optimization process and enabling extremely high protein expression levels. The method is accessible via interactive web-based software. (more...)

Augmented reality (AR) technologies have improved drastically in the recent years due to the advances in tracking, modeling and rendering techniques. However, these improvements often comes at the cost of increased startup costs, as these techniques require expensive hardware and careful calibration, hindering experimentation of AR by potential casual users. (more...)

Microarrays are used as a high throughput biochemistry technique for generating data about the quantity of mRNA expressed by each gene in cells of an organism under a set of conditions. The data that is generated, commonly known as a gene expression profile, can be used to infer global cellular activities that would be hard to describe otherwise. However, a problem that arises is that the data tends to be large and complex, making it difficult to analyze and interpret. One way to distill information from microarray data is through the use of correlation. Correlation is a traditional way of summarizing the relationship between any two variables in a system after the collection of empirical data. The term “liquid association” is used to conceptualize the internal evolution of co-expression patterns for a pair of genes in response to constant changes in the cellular state variables. But in extremely complex systems, correlation is hard to observe due to the many variables interacting with each other. There is a need for a bioinformatics tool to help with genomic research by analyzing and interpreting the large number of data involving multiple variables. (more...)

Many scheduling algorithms for time division multiple access (TDMA) have proposed to achieve collision-free transmissions of data frames within each time-slot of a single communication channel in multi-hop packet radio networks. A scheduled-access approach consists of establishing transmission schedules in a way that eliminates collisions and achieves efficient spatial reuse of the available bandwidth. Efficient scheduling with channel reuse can render much higher channel utilization than such fixed assignment approaches as TDMA and frequency division multiple access (FDMA). (more...)

Current medium-access control (MAC) protocols for wireless networks are based on collision-avoidance handshakes between sender and receiver. Most of these systems are based upon a sender-initiated handshake, in which the sender uses a short control packet to ask the receiver for permission to transmit and then only transmits if the receiver sends a clear-to-send notification. However, under high-traffic conditions, an influx of control packets can adversely affect the network. (more...)

Present Internet applications are likely to operate over paths that either exhibit a high degree of asymmetry or appear asymmetric due to significant load on the reverse data path. Under such conditions, the transmission control protocol (TCP) method of counting messages that acknowledge correctly received data (ACKs) results in significant underutilization of the link with higher capacity due to loss of ACKs on the slow link. In addition, ACK loss leads to outbursts of data traffic on the forward path. As a result, networks need an improved congestion control algorithm that is resilient to ACK loss. (more...)

Business activities are increasingly being conducted via the Internet. These applications, such as financial services, securities exchanges, and emergency services will require reliable Internet connectivity. On-demand routing protocols provide this reliability by allowing for multiple links with separate gateway links to the Internet. However, current systems are subject to the counting-to-infinity problem, which can decrease network performance. For example, when a destination fails or becomes unreachable from a network component, a source trying to obtain a path to the destination finds that its flood-search for the destination fails. It is unable to determine the mode of failure and may continue to repeat a search for an unreachable destination, which causes congestion due to the repeated queries. As a result, current systems require external mechanisms to stop sources from sending unnecessary queries. However, difficulties in these systems arise in determining the length of hold-down times and how many times a source should persist in requesting a destination path. (more...)

A content-based image retrieval system returns images based on their similarity to the query image. Most of these systems determine this similarity based on perceptual features, such as color shape and texture, but in doing so do not reflect the characteristics of the human visual process. They are unable to adjust to the environment and visual goals of the user, which can limit the effectiveness of the search. (more...)

Currently, the majority of methods used for efficiently supporting many-to-many communication (multicasting) in computer networks involve routing trees. Multicast routing trees (multicast trees for short) achieve efficient and simple transfer by forcing a single path between any pair of routers. Accordingly, if multiple sources must transmit information to the same set of destinations, using routing trees requires that either a shared multicast tree be used for all sources or that a separate multicast tree be established for each source. Using a shared multicast tree has the disadvantage that packets are distributed to the multicast group along paths that can be much longer than the shortest paths from sources to receivers. Using a separate multicast tree for each source of each multicast group leads to scaling difficulties. In addition, because trees provide minimal connectivity among the members of a multicast group, the failure of any link in the tree partitions the group and requires the routers involved to reconfigure the tree. During periods of routing-table instability, routers may be forced to stop forwarding packets while they wait for the multicast routing tree to be reconstructed. (more...)

Monitoring gene expression using high-density microarrays is a frequently-used technique in the study of cell functions and the associated biochemical pathways, candidate gene identification, cellular response to drug compounds, and classification of disease states. Because many important decisions as to whether a gene should be pursued as a candidate for a particular biological system under study are based on determined expression ratios as well as on determined differential expression, processes that provide for more accurate estimates of these derived statistics can be valuable to users of oligonucleotide array technology. Conventional normalization methods include 1) linear normalization and nonlinear regression, and 2) methods using housekeeping genes or staggered spike-in controls. These methods have drawbacks, however. The linear normalization technique does not account well for nonlinear relations. Non-linear regression can be inadequate if the expression profiles of the various arrays vary greatly from each other. Finally, many of the genes conventionally used as housekeeping genes have ranges of differential expression similar to other genes whose differential expression patterns are deemed biologically relevant to the system under study. (more...)

The explosion of the Internet has spawned a variety of video-based services over packet networks, such as streaming video and video-on-demand. Many of these applications require, or can benefit from, the network's ability to provide Quality-of-Service (QoS) guarantees. The QoS guarantees are usually in the form of bandwidth, end-to-end delay, or loss rate experienced by the traffic system. The loss curve of a video source characterizes the loss rate of the video stream generated by the source as a function of the allocated buffer size for a given transmission rate. The loss curve is useful in the optimal allocation of resources when the video stream is transmitted over a packet network so that the desired tradeoff can be reached among the loss rate, bandwidth, and the buffer space to be allocated. (more...)

Digital watermarking can provide security and protection for multimedia data by encoding user or other copyright information directly in the data. Of primary concern in digital watermarking is the recovery of image signatures even when the image has been changed by image-processing operations. Data hiding is a generalization of watermarking wherein perceptually invisible changes are made to the image pixels for embedding additional information in the data. Data hiding can be used to embed control or reference information in digital media for applications such as tracking the use of a particular pay-per-view video or billing for commercials in audio/video broadcasts. Unlike traditional encryption methods where it is obvious that something is encoded, perceptually invisible data hiding in images/video offers an alternative where it is difficult for an unauthorized person to detect or decode the hidden content. (more...)

There are many instances when it is desirable to remove an underlying operating frequency from an output signal. When the frequency range is somewhat known, this removal is relatively straightforward using a stagger-tuned notch filter. Stagger-tuned notch filters, however, introduce considerable phase lag and when the frequencies are grossly unknown, unstable, or both, so much phase lag is introduced as to make these filters unsuitable for a very important application: closed-loop control. A very narrow adaptive notch filter can be used to greatly reduce the phase lag, however, this introduces a new difficulty. A very narrow notch filter must be an infinite impulse response (IIR) filter, hence it must be recursive. This in turn makes the adaptive tracking of the notch frequency of the filter unstable, again making the situation unsuitable for closed-loop control. (more...)

Many future applications of computer networks such as teleconferencing (interactive voice and video), distance education, and remote collaboration will rely on the ability of networks to provide "Quality of Service" (QoS) guarantees. These guarantees are usually in the form of bounds on end-to-end delay, bandwidth, delay jitter, packet loss rate, or a combination of these parameters. Several shaping and scheduling algorithms for packet networks have been proposed; however, schemes that provide for QoS guarantees incur a prohibitively expensive implementation cost. (more...)