Showing papers by "SRI International published in 2005"

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

Abstract: The BioCyc database collection is a set of 160 pathway/genome databases (PGDBs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. Each PGDB in the BioCyc collection describes the genome and predicted metabolic network of a single organism, inferred from the MetaCyc database, which is a reference source on metabolic pathways from multiple organisms. In addition, each bacterial PGDB includes predicted operons for the corresponding species. The BioCyc collection provides a unique resource for computational systems biology, namely global and comparative analyses of genomes and metabolic networks, and a supplement to the BioCyc resource of curated PGDBs. The Omics viewer available through the BioCyc website allows scientists to visualize combinations of gene expression, proteomics and metabolomics data on the metabolic maps of these organisms. This paper discusses the computational methodology by which the BioCyc collection has been expanded, and presents an aggregate analysis of the collection that includes the range of number of pathways present in these organisms, and the most frequently observed pathways. We seek scientists to adopt and curate individual PGDBs within the BioCyc collection. Only by harnessing the expertise of many scientists we can hope to produce biological databases, which accurately reflect the depth and breadth of knowledge that the biomedical research community is producing.

Activity recognition and abnormality detection with the switching hidden semi-Markov model

Abstract: This paper addresses the problem of learning and recognizing human activities of daily living (ADL), which is an important research issue in building a pervasive and smart environment. In dealing with ADL, we argue that it is beneficial to exploit both the inherent hierarchical organization of the activities and their typical duration. To this end, we introduce the switching hidden semi-markov model (S-HSMM), a two-layered extension of the hidden semi-Markov model (HSMM) for the modeling task. Activities are modeled in the S-HSMM in two ways: the bottom layer represents atomic activities and their duration using HSMMs; the top layer represents a sequence of high-level activities where each high-level activity is made of a sequence of atomic activities. We consider two methods for modeling duration: the classic explicit duration model using multinomial distribution, and the novel use of the discrete Coxian distribution. In addition, we propose an effective scheme to detect abnormality without the need for training on abnormal data. Experimental results show that the S-HSMM performs better than existing models including the flat HSMM and the hierarchical hidden Markov model in both classification and abnormality detection tasks, alleviating the need for presegmented training data. Furthermore, our discrete Coxian duration model yields better computation time and generalization error than the classic explicit duration model.

Computational prediction of human metabolic pathways from the complete human genome

Abstract: Background We present a computational pathway analysis of the human genome that assigns enzymes encoded therein to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary first step toward quantitative modeling of metabolism.

The complete genome sequence of Francisella tularensis, the causative agent of tularemia.

Abstract: Francisella tularensis is one of the most infectious human pathogens known. In the past, both the former Soviet Union and the US had programs to develop weapons containing the bacterium. We report the complete genome sequence of a highly virulent isolate of F. tularensis (1,892,819 bp). The sequence uncovers previously uncharacterized genes encoding type IV pili, a surface polysaccharide and iron-acquisition systems. Several virulence-associated genes were located in a putative pathogenicity island, which was duplicated in the genome. More than 10% of the putative coding sequences contained insertion-deletion or substitution mutations and seemed to be deteriorating. The genome is rich in IS elements, including IS630 Tc-1 mariner family transposons, which are not expected in a prokaryote. We used a computational method for predicting metabolic pathways and found an unexpectedly high proportion of disrupted pathways, explaining the fastidious nutritional requirements of the bacterium. The loss of biosynthetic pathways indicates that F. tularensis is an obligate host-dependent bacterium in its natural life cycle. Our results have implications for our understanding of how highly virulent human pathogens evolve and will expedite strategies to combat them.

The Children and Youth We Serve A National Picture of the Characteristics of Students With Emotional Disturbances Receiving Special Education

Abstract: This article provides a national perspective of children and youth with emotional disturbances (ED) served in special education using data from the Special Education Elementary Longitudinal Study and the National LongitudinalTransition Study—2. Data sources comprise teachers,school records, the students, and their parents. Results indicate that children and youth with ED live in households in which multiple risk factors exist for poor life outcomes. As a group, these children and youth have serious and multiple impairments that include an array of emotional disabilities, poor communication skills, and low academic achievement. There is a considerable gap between initial identification of problems and the onset of service delivery, a high rate of suspension and expulsion, and an unstable school environment. Parents of children and youth with ED work harder to secure services for their children and are less satisfied with services than parents of children in other disability groups. Implications of the find...

Neurocircuitry in alcoholism: a substrate of disruption and repair

Abstract: The chronic, excessive consumption of alcohol results in significant modification of selective neural systems of the brain structure, physiology, and function. Quantitative MR structural imaging, diffusion tensor imaging (DTI), and functional MRI (fMRI), together with neuropsychological challenges, have enabled rigorous in vivo characterization of the results of alcoholism on the brain in the human condition. Neuroimaging has also enabled longitudinal study for the examination of alcoholism’s dynamic course through periods of drinking and sobriety. Controlled studies have revealed compelling evidence for alcohol-related brain structural and functional modification—some longstanding, some transient, and some compensatory. Patterns of circuitry disruption identified through structural and functional MRI studies suggest a central role for degradation of frontocerebellar neuronal nodes and connecting circuitry affecting widespread brain regions and contributing to alcoholism’s salient, enduring, and debilitating cognitive and motor deficits—executive dysfunction, visuospatial impairment, and ataxia.

Students Becoming Chemists: Developing Representationl Competence

Abstract: This chapter examines the role that representations and visualizations can play in the chemical curriculum. Two types of curricular goals are examined: students’ acquisition of important chemical concepts and principles and students’ participation in the investigative practices of chemistry—“students becoming chemists.” Literature in learning theory and research support these two goals and this literature is reviewed. The first goal relates to cognitive theory and the way that representations and visualizations can support student understanding of concepts related to molecular entities and processes that are not otherwise available for direct perception. The second goal relates to situative theory and the role that representations and visualizations play in development of representational competence and the social and physical processes of collaboratively constructing an understanding of chemical processes in the laboratory. We analyze research on computer-based molecular modeling, simulations, and animations from these two perspectives and make recommendations for instruction and future research.

National policies that connect ICT-based education reform to economic and social development

Abstract: Information and communication technology (ICT) is a principal driver of economic development and social change, worldwide. In many countries, the need for economic and social development is used to justify investments in educational reform and in educational ICT. Yet the connections between national development goals and ICT-based education reform are often more rhetorical than programmatic. This paper identifies the factors that influence economic growth and shows how they supported economic and social development in three national case studies: Singapore, Finland, and Egypt. It describes a systemic framework of growth factors and types of development that can be used to analyze national policies and connect ICT-based education reform to national economic and social development goals. And it discusses how the coordination of policies within and across ministries can support a nation’s efforts to improve economic and social conditions. The paper highlights special concerns and challenges of developing countries.

Learning and detecting activities from movement trajectories using the hierarchical hidden Markov model

Abstract: Directly modeling the inherent hierarchy and shared structures of human behaviors, we present an application of the hierarchical hidden Markov model (HHMM) for the problem of activity recognition. We argue that to robustly model and recognize complex human activities, it is crucial to exploit both the natural hierarchical decomposition and shared semantics embedded in the movement trajectories. To this end, we propose the use of the HHMM, a rich stochastic model that has been recently extended to handle shared structures, for representing and recognizing a set of complex indoor activities. Furthermore, in the need of real-time recognition, we propose a Rao-Blackwellised particle filter (RBPF) that efficiently computes the filtering distribution at a constant time complexity for each new observation arrival. The main contributions of this paper lie in the application of the shared-structure HHMM, the estimation of the model's parameters at all levels simultaneously, and a construction of an RBPF approximate inference scheme. The experimental results in a real-world environment have confirmed our belief that directly modeling shared structures not only reduces computational cost, but also improves recognition accuracy when compared with the tree HHMM and the flat HMM.

Method and apparatus for total situational awareness and monitoring

Abstract: A sentient system combines detection, tracking, and immersive visualization of a cluttered and crowded environment, such as an office building, terminal, or other enclosed site using a network of stereo cameras A guard monitors the site using a live 3D model, which is updated from different directions using the multiple video streams As a person moves within the view of a camera, the system detects its motion and tracks the person's path, it hands off the track to the next camera when the person goes out of that camera's view Multiple people can be tracked simultaneously both within and across cameras, with each track shown on a map display The track system includes a track map browser that displays the tracks of all moving objects as well as a history of recent tracks and a video flashlight viewer that displays live immersive video of any person that is being tracked

Multiradar observations of the polar tongue of ionization

Abstract: [1] We present a global view of large-scale ionospheric disturbances during the main phase of a major geomagnetic storm. We find that the low-latitude, auroral, and polar latitude regions are coupled by processes that redistribute thermal plasma throughout the system. For the large geomagnetic storm on 20 November 2003, we examine data from the high-latitude incoherent scatter radars at Millstone Hill, Sondrestrom, and EISCAT Tromso, with SuperDARN HF radar observations of the high-latitude convection pattern and DMSP observations of in situ plasma parameters in the topside ionosphere. We combine these with north polar maps of stormtime plumes of enhanced total electron content (TEC) derived from a network of GPS receivers. The polar tongue of ionization (TOI) is seen to be a continuous stream of dense cold plasma entrained in the global convection pattern. The dayside source of the TOI is the plume of storm enhanced density (SED) transported from low latitudes in the postnoon sector by the subauroral disturbance electric field. Convection carries this material through the dayside cusp and across the polar cap to the nightside where the auroral F region is significantly enhanced by the SED material. The three incoherent scatter radars provided full altitude profiles of plasma density, temperatures, and vertical velocity as the TOI plume crossed their different positions, under the cusp, in the center of the polar cap, and at the midnight oval/polar cap boundary. Greatly elevated F peak density (>1.5E12 m 3 ) and low electron and ion temperatures (2500 K at the F peak altitude) characterize the SED/TOI plasma observed at all points along its high-latitude trajectory. For this event, SED/TOI F region TEC (150–1000 km) was 50 TECu both in the cusp and in the center of the polar cap. Large, upward directed fluxes of O+ (>1.E14 m 2 s 1 ) were observed in the topside ionosphere

Corpus Callosal Microstructural Integrity Influences Interhemispheric Processing: A Diffusion Tensor Imaging Study

Abstract: Normal aging and chronic alcoholism result in disruption of brain white matter microstructure that does not typically cause complete lesions but may underlie degradation of functions requiring interhemispheric information transfer. We examined whether the microstructural integrity of the corpus callosum assessed with diffusion tensor imaging (DTI) would relate to interhemispheric processing speed. DTI yields estimates of fractional anisotropy (FA), a measure of orientation and intravoxel coherence of water diffusion usually in white matter fibers, and diffusivity ( ), a measure of the amount of intracellular and extracellular fluid diffusion. We tested the hypothesis that FA and would be correlated with (i) the crossed--uncrossed difference (CUD), testing visuomotor interhemispheric transfer; and (ii) the redundant targets effect (RTE), testing parallel processing of visual information presented to each cerebral hemisphere. FA was lower and higher in alcoholics than in controls. In controls but not alcoholics, large CUDs correlated with low FA and high in total corpus callosum and regionally in the genu and splenium. In alcoholics but not controls, small RTEs, elicited with equiluminant stimuli, correlated with low FA in genu and splenium and high in the callosal body. The results provide in vivo evidence for disruption of corpus callosum microstructure in normal aging and alcoholism that has functional ramifications for efficiency in interhemispheric processing.

Active preference learning for personalized calendar scheduling assistance

Abstract: We present PLIANT, a learning system that supports adaptive assistance in an open calendaring system. PLIANT learns user preferences from the feedback that naturally occurs during interactive scheduling. It contributes a novel application of active learning in a domain where the choice of candidate schedules to present to the user must balance usefulness to the learning module with immediate benefit to the user. Our experimental results provide evidence of PLIANT's ability to learn user preferences under various conditions and reveal the tradeoffs made by the different active learning selection strategies.

Three-dimensional average-shape atlas of the honeybee brain and its applications

Abstract: The anatomical substrates of neural nets are usually composed from reconstructions of neurons that were stained in different preparations. Realistic models of the structural relationships between neurons require a common framework. Here we present 3-D reconstructions of single projection neurons (PN) connecting the antennal lobe (AL) with the mushroom body (MB) and lateral horn, groups of intrinsic mushroom body neurons (type 5 Kenyon cells), and a single mushroom body extrinsic neuron (PE1), aiming to compose components of the olfactory pathway in the honeybee. To do so, we constructed a digital standard atlas of the bee brain. The standard atlas was created as an average-shape atlas of 22 neuropils, calculated from 20 individual immunostained whole-mount bee brains. After correction for global size and positioning differences by repeatedly applying an intensity-based nonrigid registration algorithm, a sequence of average label images was created. The results were qualitatively evaluated by generating average gray-value images corresponding to the average label images and judging the level of detail within the labeled regions. We found that the first affine registration step in the sequence results in a blurred image because of considerable local shape differences. However, already the first nonrigid iteration in the sequence corrected for most of the shape differences among individuals, resulting in images rich in internal detail. A second iteration improved on that somewhat and was selected as the standard. Registering neurons from different preparations into the standard atlas reveals 1) that the m-ACT neuron occupies the entire glomerulus (cortex and core) and overlaps with a local interneuron in the cortical layer; 2) that, in the MB calyces and the lateral horn of the protocerebral lobe, the axon terminals of two identified m-ACT neurons arborize in separate but close areas of the neuropil; and 3) that MB-intrinsic clawed Kenyon cells (type 5), with somata outside the calycal cups, project to the peduncle and lobe output system of the MB and contact (proximate) the dendritic tree of the PE1 neuron at the base of the vertical lobe. Thus the standard atlas and the procedures applied for registration serve the function of creating realistic neuroanatomical models of parts of a neural net. The Honeybee Standard Brain is accessible at www.neurobiologie.fu-berlin.de/beebrain.

VERL: an ontology framework for representing and annotating video events

Abstract: The notion of "events" is extremely important in characterizing the contents of video. An event is typically triggered by some kind of change of state captured in the video, such as when an object starts moving. The ability to reason with events is a critical step toward video understanding. This article describes the findings of a recent workshop series that has produced an ontology framework for representing video events-called Video Event Representation Language (VERL) -and a companion annotation framework, called Video Event Markup Language (VEML). One of the key concepts in this work is the modeling of events as composable, whereby complex events are constructed from simpler events by operations such as sequencing, iteration, and alternation. The article presents an extensible event and object ontology expressed in VERL and discusses a detailed example of applying VERL and VEML to the description of a "tailgating" event in surveillance video.

The Special Education Elementary Longitudinal Study and the National Longitudinal Transition Study: Study Designs and Implications for Children and Youth With Emotional Disturbance

Abstract: The purposes of this article are to (a) describe the design features of two longitudinal studies,the Special Education Elementary Longitudinal Study (SEELS) and the National Longitudinal Transition Study—2 (NLTS2) and (b) outline their potential implications for policy, practice, research, advocacy, and system development for children and youth with emotional disturbances (ED). We begin by reviewing the role of longitudinal research and its importance in building the knowledge base regarding these children and youth. A review of illustrative longitudinal studies conducted on children and youth with ED points to the potential of a longitudinal design for providing much needed information but also reveals the limitations and inconsistencies in both the samples and methods of existing studies that hamper development of policy and practice. SEELS and NLTS2 are offered as exemplars of the type of studies needed to supply critical information to the field. We describe key features of these studies and how they ...

Method and apparatus for combating malicious code

Abstract: A method and apparatus are provided for combating malicious code. In one embodiment, a method for combating malicious code in a network includes implementing a resource-limiting technique to slow a propagation of the malicious code and implementing a leap-ahead technique in parallel with the resource-limiting technique to defend against the malicious code reaching a full saturation potential in the network.

Mechanical meta-materials

Abstract: The present invention provides meta-materials with an actively controllable mechanical property. The meta-material includes a deformable structure and a set of activation elements. The activation elements are controllable between multiple states. The meta-material includes a first value for a mechanical property when one or more of the activation elements is in the first activation state and includes a second value for the mechanical property when the activation elements have been activated to the second activation state. In one aspect, the meta-material resembles a composite material where the connectivity between the component materials or shape and arrangement of the component materials is dynamically controllable so as to affect a mechanical property of the meta-material.

Spontaneous speech: how people really talk and why engineers should care.

Abstract: Spontaneous conversation is optimized for human-human communication, but differs in some important ways from the types of speech for which human language technology is often developed. This overview describes four fundamental properties of spontaneousspeech that present challenges for spoken language applications because they violate assumptions often applied in automatic processing technology.

MLLR transforms as features in speaker recognition.

Abstract: We explore the use of adaptation transforms employed in speech recognition systems as features for speaker recognition. This approach is attractive because, unlike standard framebased cepstral speaker recognition models, it normalizes for the choice of spoken words in text-independent speaker verification. Affine transforms are computed for the Gaussian means of the acoustic models used in a recognizer, using maximum likelihood linear regression (MLLR). The high-dimensional vectors formed by the transform coefficients are then modeled as speaker features using support vector machines (SVMs). The resulting speaker verification system is competitive, and in some cases significantly more accurate, than state-of-the-art cepstral gaussian mixture and SVM systems. Further improvements are obtained by combining baseline and MLLR-based systems.

Alcoholic neurobiology: changes in dependence and recovery.

Abstract: This article presents the proceedings of a symposium held at the meeting of the International Society for Biomedical Research on Alcoholism (ISBRA) in Mannheim, Germany, in October, 2004. Chronic alcoholism follows a fluctuating course, which provides a naturalistic experiment in vulnerability, resilience, and recovery of human neural systems in response to presence, absence, and history of the neurotoxic effects of alcoholism. Alcohol dependence is a progressive chronic disease that is associated with changes in neuroanatomy, neurophysiology, neural gene expression, psychology, and behavior. Specifically, alcohol dependence is characterized by a neuropsychological profile of mild to moderate impairment in executive functions, visuospatial abilities, and postural stability, together with relative sparing of declarative memory, language skills, and primary motor and perceptual abilities. Recovery from alcoholism is associated with a partial reversal of CNS deficits that occur in alcoholism. The reversal of deficits during recovery from alcoholism indicates that brain structure is capable of repair and restructuring in response to insult in adulthood. Indirect support of this repair model derives from studies of selective neuropsychological processes, structural and functional neuroimaging studies, and preclinical studies on degeneration and regeneration during the development of alcohol dependence and recovery from dependence. Genetics and brain regional specificity contribute to unique changes in neuropsychology and neuroanatomy in alcoholism and recovery. This symposium includes state-of-the-art presentations on changes that occur during active alcoholism as well as those that may occur during recovery-abstinence from alcohol dependence. Included are human neuroimaging and neuropsychological assessments, changes in human brain gene expression, allelic combinations of genes associated with alcohol dependence and preclinical studies investigating mechanisms of alcohol induced neurotoxicity, and neuroprogenetor cell expansion during recovery from alcohol dependence.

Fast generation of digitally reconstructed radiographs using attenuation fields with application to 2D-3D image registration

Abstract: Generation of digitally reconstructed radiographs (DRRs) is computationally expensive and is typically the rate-limiting step in the execution time of intensity-based two-dimensional to three-dimensional (2D-3D) registration algorithms. We address this computational issue by extending the technique of light field rendering from the computer graphics community. The extension of light fields, which we call attenuation fields (AFs), allows most of the DRR computation to be performed in a preprocessing step; after this precomputation step, DRRs can be generated substantially faster than with conventional ray casting. We derive expressions for the physical sizes of the two planes of an AF necessary to generate DRRs for a given X-ray camera geometry and all possible object motion within a specified range. Because an AF is a ray-based data structure, it is substantially more memory efficient than a huge table of precomputed DRRs because it eliminates the redundancy of replicated rays. Nonetheless, an AF can require substantial memory, which we address by compressing it using vector quantization. We compare DRRs generated using AFs (AF-DRRs) to those generated using ray casting (RC-DRRs) for a typical C-arm geometry and computed tomography images of several anatomic regions. They are quantitatively very similar: the median peak signal-to-noise ratio of AF-DRRs versus RC-DRRs is greater than 43 dB in all cases. We perform intensity-based 2D-3D registration using AF-DRRs and RC-DRRs and evaluate registration accuracy using gold-standard clinical spine image data from four patients. The registration accuracy and robustness of the two methods is virtually identical whereas the execution speed using AF-DRRs is an order of magnitude faster.

On the enigma of day-to-day variability in equatorial spread F

Abstract: [1] We show that large-scale wave structure (LSWS), in plasma density in the bottomside F layer, is a hitherto unheralded contributor to the long-standing enigma of day-to-day variability in equatorial spread F (ESF). Little is known about LSWS; it seems to appear in altitude near a vertical shear in zonal plasma drift, during the post-sunset rise of the F layer, and its growth via an interchange instability appears to predispose quasi-periodically spaced regions to development of plasma bubbles. First indications are that LSWS development is necessary and sufficient for ESF occurrence. We suggest that variability in LSWS development, perhaps together with the shear in zonal drift, may contribute to day-to-day ESF variability. A need revealed by this study is that a cluster of distributed sensors, not isolated ones, is necessary to pursue the problem of day-to-day variability.

Thirty-six-month outcomes for families of children who have disabilities and participated in early intervention.

Abstract: Objective. Infants and toddlers with disabilities in the United States and their families are eligible for early intervention services under Part C of the Individuals With Disabilities Education Act. The purpose of this study was to assess family outcomes at the end of early intervention (near the child’s third birthday). Methods. A nationally representative sample of 2586 parents in 20 states completed a 40-minute telephone interview on or near their child’s third birthday. This article summarizes data related to perceived family outcomes at the end of early intervention. Results. At the end of early intervention, most parents felt competent in caring for their children, advocating for services, and gaining access to formal and informal supports. They also were generally optimistic about the future. Most (82%) parents believed that their family was better off as a result of early intervention. Parents were somewhat less positive in their perceived ability to deal with their child’s behavior problems or gain access to community resources, and lower family outcome scores were found for parents of minority children, children with health problems, and children who were living with a single adult. Conclusion. Results suggest that Part C early intervention provides important supports for families of young children with disabilities. The findings reinforce the need for experimental research to identify factors that are most likely to lead to successful outcomes for all families. In the meantime, early identification and expeditious referral are important so that maximum benefit can be realized for children with disabilities and their families.

Method and apparatus for aligning video to three-dimensional point clouds

Abstract: A method and apparatus for performing two-dimensional video alignment onto three-dimensional point clouds. The system recovers camera pose from camera video, determines a depth map, converts the depth map to a Euclidean video point cloud, and registers two-dimensional video to the three-dimensional point clouds.

Method and apparatus for stereo, multi-camera tracking and RF and video track fusion

Abstract: A unified approach, a fusion technique, a space-time constraint, a methodology, and system architecture are provided. The unified approach is to fuse the outputs of monocular and stereo video trackers, RFID and localization systems and biometric identification systems. The fusion technique is provided that is based on the transformation of the sensory information from heterogeneous sources into a common coordinate system with rigorous uncertainties analysis to account for various sensor noises and ambiguities. The space-time constraint is used to fuse different sensor using the location and velocity information. Advantages include the ability to continuously track multiple humans with their identities in a large area. The methodology is general so that other sensors can be incorporated into the system. The system architecture is provided for the underlying real-time processing of the sensors.