Showing papers by "North Carolina State University published in 2003"
Baylor College of Medicine1, Chinese Academy of Sciences2, Chinese National Human Genome Center3, University of Hong Kong4, The Chinese University of Hong Kong5, Hong Kong University of Science and Technology6, Illumina7, McGill University8, Washington University in St. Louis9, University of California, San Francisco10, Wellcome Trust Sanger Institute11, Beijing Normal University12, Health Sciences University of Hokkaido13, Shinshu University14, University of Tsukuba15, Howard University16, University of Ibadan17, Case Western Reserve University18, University of Utah19, Cold Spring Harbor Laboratory20, Johns Hopkins University21, University of Oxford22, North Carolina State University23, National Institutes of Health24, Massachusetts Institute of Technology25, Chinese Academy of Social Sciences26, Kyoto University27, Nagasaki University28, Wellcome Trust29, Genome Canada30, Foundation for the National Institutes of Health31, University of Maryland, Baltimore32, Vanderbilt University33, Stanford University34, University of California, Berkeley35, New York University36, University of Oklahoma37, University of New Mexico38, Université de Montréal39, University of California, Los Angeles40, University of Michigan41, University of Wisconsin-Madison42, London School of Economics and Political Science43, Genetic Alliance44, GlaxoSmithKline45, University of Washington46, Harvard University47, University of Chicago48, Fred Hutchinson Cancer Research Center49, University of Tokyo50
TL;DR: The HapMap will allow the discovery of sequence variants that affect common disease, will facilitate development of diagnostic tools, and will enhance the ability to choose targets for therapeutic intervention.
Abstract: The goal of the International HapMap Project is to determine the common patterns of DNA sequence variation in the human genome and to make this information freely available in the public domain. An international consortium is developing a map of these patterns across the genome by determining the genotypes of one million or more sequence variants, their frequencies and the degree of association between them, in DNA samples from populations with ancestry from parts of Africa, Asia and Europe. The HapMap will allow the discovery of sequence variants that affect common disease, will facilitate development of diagnostic tools, and will enhance our ability to choose targets for therapeutic intervention.
5,926 citations
TL;DR: The basic patterns of LD in plants will be better understood as more species are analyzed, and association mapping has been exploited to dissect quantitative trait loci (QTL).
Abstract: Future advances in plant genomics will make it possible to scan a genome for polymorphisms associated with qualitative and quantitative traits. Before this potential can be realized, we must understand the nature of linkage disequilibrium (LD) within a genome. LD, the nonrandom association of alleles at different loci, plays an integral role in association mapping, and determines the resolution of an association study. Recently, association mapping has been exploited to dissect quantitative trait loci (QTL). With the exception of maize and Arabidopsis, little research has been conducted on LD in plants. The mating system of the species (selfing versus outcrossing), and phenomena such as population structure and recombination hot spots, can strongly influence patterns of LD. The basic patterns of LD in plants will be better understood as more species are analyzed.
1,495 citations
TL;DR: The theoretical basis for modeling univariate traffic condition data streams as seasonal autoregressive integrated moving average processes as well as empirical results using actual intelligent transportation system data are presented and found to be consistent with the theoretical hypothesis.
Abstract: This article presents the theoretical basis for modeling univariate traffic condition data streams as seasonal autoregressive integrated moving average processes. This foundation rests on the Wold decomposition theorem and on the assertion that a one-week lagged first seasonal difference applied to discrete interval traffic condition data will yield a weakly stationary transformation. Moreover, empirical results using actual intelligent transportation system data are presented and found to be consistent with the theoretical hypothesis. Conclusions are given on the implications of these assertions and findings relative to ongoing intelligent transportation systems research, deployment, and operations.
1,406 citations
27 Oct 2003
TL;DR: In this paper, a general framework for establishing pairwise keys between sensors on the basis of a polynomial-based key predistribution protocol is presented, and two efficient instantiations of the general framework are presented: a random subset assignment key pre-distribution scheme and a grid-based pre-disposition scheme.
Abstract: Pairwise key establishment is a fundamental security service in sensor networks; it enables sensor nodes to communicate securely with each other using cryptographic techniques. However, due to the resource constraints on sensors, it is infeasible to use traditional key management techniques such as public key cryptography and key distribution center (KDC). To facilitate the study of novel pairwise key predistribution techniques, this paper presents a general framework for establishing pairwise keys between sensors on the basis of a polynomial-based key predistribution protocol [2]. This paper then presents two efficient instantiations of the general framework: a random subset assignment key predistribution scheme and a grid-based key predistribution scheme. The analysis in this paper indicates that these two schemes have a number of nice properties, including high probability (or guarantee) to establish pairwise keys, tolerance of node captures, and low communication overhead. Finally, this paper presents a technique to reduce the computation at sensors required by these schemes.
1,391 citations
TL;DR: In this article, a review of the use of 1-methylcyclopropene (1-MCP) as an inhibitor of ethylene action is presented, which is a tool that can help scientists make major advances in understanding the role of the chemical in plants.
1,118 citations
TL;DR: This survey paper presents recent NCS control methodologies and the overview on NCS structures and description of network delays including characteristics and effects are covered.
1,084 citations
TL;DR: It is demonstrated that multiple trajectory classes can be estimated and appear optimal for nonnormal data even when only 1 group exists in the population.
Abstract: Growth mixture models are often used to determine if subgroups exist within the population that follow qualitatively distinct developmental trajectories. However, statistical theory developed for finite normal mixture models suggests that latent trajectory classes can be estimated even in the absence of population heterogeneity if the distribution of the repeated measures is nonnormal. By drawing on this theory, this article demonstrates that multiple trajectory classes can be estimated and appear optimal for nonnormal data even when only 1 group exists in the population. Further, the within-class parameter estimates obtained from these models are largely uninterpretable. Significant predictive relationships may be obscured or spurious relationships identified. The implications of these results for applied research are highlighted, and future directions for quantitative developments are suggested.
922 citations
TL;DR: This article proposed a cascading activation model to explain how interpretive frames activate and spread from the top level of a stratified system (the White House) to the network of nonadministration elites, and on to news organizations, their texts, and the public.
Abstract: President Bush's initial frame for the attacks of September 11, 2001, overwhelmingly dominated the news. Using that frame as a springboard, this article advances a coherent conception of framing within a new model of the relationship between government and the media in U.S. foreign policy making. The cascading activation model supplements research using the hegemony or indexing approaches. The model explains how interpretive frames activate and spread from the top level of a stratified system (the White House) to the network of nonadministration elites, and on to news organizations, their texts, and the public--and how interpretations feed back from lower to higher levels. To illustrate the model's potential, the article explores the frame challenge mounted by two journalists, Seymour Hersh and Thomas Friedman, who attempted to shift the focus from Afghanistan to Saudi Arabia. As hegemony theory predicts, 9/11 revealed yet again that media patrol the boundaries of culture and keep discord within conventio...
795 citations
TL;DR: In this paper, the authors provide guidance on the formulation of course learning objectives and assessment methods that address Outcomes 3a-3k; identify and describe instructional techniques that should effectively prepare students to achieve those outcomes by the time they graduate; and propose a strategy for integrating program-level and course-level activities when designing an instructional program to meet the requirements of the ABET engineering criteria.
Abstract: Since the new ABET accreditation system was first introduced to American engineering education in the middle 1990s as Engineering Criteria 2000, most discussion in the literature has focused on how to assess Outcomes 3a-3k and relatively little has concerned how to equip students with the skills and attitudes specified in those outcomes. This paper seeks to fill this gap. Its goals are to (1) overview the accreditation process and clarify the confusing array of terms associated with it (objectives, outcomes, outcome indicators, etc.); (2) provide guidance on the formulation of course learning objectives and assessment methods that address Outcomes 3a-3k; (3) identify and describe instructional techniques that should effectively prepare students to achieve those outcomes by the time they graduate; and (4) propose a strategy for integrating program-level and course-level activities when designing an instructional program to meet the requirements of the ABET engineering criteria.
790 citations
TL;DR: The ability of peptide-modified gold nanoparticles to target the nucleus of HepG2 cells was explored and nuclear targeting was more efficient when the two signals were attached to nanoparticles as separate short pieces versus one long peptide.
Abstract: The ability of peptide-modified gold nanoparticles to target the nucleus of HepG2 cells was explored. Five peptide/nanoparticle complexes were investigated, particles modified with (1) the nuclear localization signal (NLS) from the SV 40 virus; (2) the adenovirus NLS; (3) the adenovirus receptor-mediated endocytosis (RME) peptide; (4) one long peptide containing the adenovirus RME and NLS; and (5) the adenovirus RME and NLS peptides attached to the nanoparticle as separate pieces. Gold nanoparticles were used because they are easy to identify using video-enhanced color differential interference contrast microscopy, and they are excellent scaffolds from which to build multifunctional nuclear targeting vectors. For example, particles modified solely with NLS peptides were not able to target the nucleus of HepG2 cells from outside the plasma membrane, because they either could not enter the cell or were trapped in endosomes. The combination of NLS/RME particles (4) and (5) did reach the nucleus; however, nuc...
766 citations
Abstract: This study examines what drives customers' use of an online channel in a relational, multichannel environment. The authors propose a conceptual model of the determinants of online channel use and overall satisfaction with the service provider. They then conduct two large-scale studies in different service contexts to test the model. The results show that Web site design characteristics affect customer evaluations of online channel service quality and risk, which in turn drive online channel use. Customers' overall satisfaction with the service provider is determined by the service quality provided through both the online channel and the traditional channel. The results offer insights into the trade-offs that multichannel service providers face as they attempt to influence online channel use while maintaining or enhancing overall customer satisfaction.
TL;DR: This paper analyzed the role of perceived authenticity as a measure of product quality and as a determinant of tourist satisfaction, and found that high perception of authenticity can be achieved even when the event is staged far away from the original source of the cultural tradition.
TL;DR: Body weight, feed consumption, and mortality were measured in the 1957 Athens-Canadian Randombred Control (ACRBC) strain and in the 2001 Ross 308 strain of broilers when fed representative 1957 and 2001 diets.
TL;DR: Results reveal that top management support and training are positively related to user satisfaction, while perceived complexity of ERP and competitive pressure show a negative relationship.
TL;DR: The ease of implementation and flexibility of the heuristic show the potential of this new approach, which utilizes an attraction-repulsion mechanism to move the sample points towards the optimality.
Abstract: This paper proposes a new heuristic for global optimization. The method utilizes an attraction-repulsion mechanism to move the sample points towards the optimality. The proposed scheme can be used either as a stand-alone approach or as an accompanying procedure for other methods. Some test results on nonlinear test functions in the category of ``minor to moderate difficulty'' are included. The ease of implementation and flexibility of the heuristic show the potential of this new approach.
New England Biolabs1, New York State Department of Health2, Columbia University3, Wayne State University4, University of Basel5, University of Toledo6, University of Edinburgh7, University of Alabama8, University of Portsmouth9, Moscow State University10, University of Illinois at Chicago11, University of Bristol12, University of Rochester13, Duke University14, University of Sheffield15, Vilnius University16, University of Giessen17, University of Copenhagen18, Hungarian Academy of Sciences19, North Carolina State University20, University of Tokyo21, Humboldt University of Berlin22, Brookhaven National Laboratory23, University of Massachusetts Medical School24, National Institutes of Health25, Indian Institute of Science26, University of Warsaw27, University of California, Santa Barbara28, State Research Center of Virology and Biotechnology VECTOR29, University of Oregon30, The Chinese University of Hong Kong31, University of Maryland, College Park32, Fred Hutchinson Cancer Research Center33, University of Wisconsin-Madison34, University of Nebraska–Lincoln35, University of Lisbon36
TL;DR: In this article, a nomenclature for restriction endonucleases, DNA methyltransferases, homing endon nucleases and related genes and gene products is described.
Abstract: A nomenclature is described for restriction endonucleases, DNA methyltransferases, homing endonucleases and related genes and gene products. It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genomes.
TL;DR: T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening the understanding of the complex evolution and ecology of phages—the most abundant and among the most ancient biological entities on Earth.
Abstract: Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages-the most abundant and among the most ancient biological entities on Earth.
TL;DR: In this article, the stability of standing, spherical accretion shocks is examined in core-collapse supernovae, star formation, and accreting white dwarfs and neutron stars.
Abstract: We examine the stability of standing, spherical accretion shocks. Accretion shocks arise in core-collapse supernovae (the focus of this paper), star formation, and accreting white dwarfs and neutron stars. We present a simple analytic model and use time-dependent hydrodynamics simulations to show that this solution is stable to radial perturbations. In two dimensions we show that small perturbations to a spherical shock front can lead to rapid growth of turbulence behind the shock, driven by the injection of vorticity from the now nonspherical shock. We discuss the ramifications this instability may have for the supernova mechanism.
Wageningen University and Research Centre1, Ludwig Maximilian University of Munich2, Yale University3, University of Texas at Austin4, Santa Fe Institute5, National Center for Genome Resources6, University of California, San Diego7, Washington University in St. Louis8, Spanish National Research Council9, North Carolina State University10, Florida State University11, Harvard University12, Michigan State University13, University of Washington14, University of New Mexico15, University of British Columbia16
TL;DR: This work focuses on the first kind of robustness—genetic robustness)—and survey three growing avenues of research: measuring genetic robustness in nature and in the laboratory; understanding the evolution of genetic robusts; and exploring the implications of genetic resilientness for future evolution.
Abstract: Robustness is the invariance of phenotypes in the face of perturbation. The robustness of phenotypes appears at various levels of biological organization, including gene expression, protein folding, metabolic flux, physiological homeostasis, development, and even organismal fitness. The mechanisms underlying robustness are diverse, ranging from thermodynamic stability at the RNA and protein level to behavior at the organismal level. Phenotypes can be robust either against heritable perturbations (e.g., mutations) or nonheritable perturbations (e.g., the weather). Here we primarily focus on the first kind of robustness-genetic robustness-and survey three growing avenues of research: (1) measuring genetic robustness in nature and in the laboratory; (2) understanding the evolution of genetic robustness; and (3) exploring the implications of genetic robustness for future evolution.
TL;DR: In this paper, the possible optimization of strength and ductility in nanocrystalline and ultrafine grained metals is assessed for microstructures with appropriate grain size distributions, and the introduction of second phase particles.
TL;DR: Two new soft X-ray scanning transmission microscopes located at the Advanced Light Source (ALS) have been designed, built and commissioned and interferometer control implemented in both microscopes allows the precise measurement of the transverse position of the zone plate relative to the sample.
Abstract: Two new soft X-ray scanning transmission microscopes located at the Advanced Light Source (ALS) have been designed, built and commissioned. Interferometer control implemented in both microscopes allows the precise measurement of the transverse position of the zone plate relative to the sample. Long-term positional stability and compensation for transverse displacement during translations of the zone plate have been achieved. The interferometer also provides low-distortion orthogonal x, y imaging. Two different control systems have been developed: a digital control system using standard VXI components at beamline 7.0, and a custom feedback system based on PC AT boards at beamline 5.3.2. Both microscopes are diffraction limited with the resolution set by the quality of the zone plates. Periodic features with 30 nm half period can be resolved with a zone plate that has a 40 nm outermost zone width. One microscope is operating at an undulator beamline (7.0), while the other is operating at a novel dedicated bending-magnet beamline (5.3.2), which is designed specifically to illuminate the microscope. The undulator beamline provides count rates of the order of tens of MHz at high-energy resolution with photon energies of up to about 1000 eV. Although the brightness of a bending-magnet source is about four orders of magnitude smaller than that of an undulator source, photon statistics limited operation with intensities in excess of 3 MHz has been achieved at high energy resolution and high spatial resolution. The design and performance of these microscopes are described.
TL;DR: This article provides exact upper bounds on the throughput of any node in a WMN for a given topology and the set of active nodes, and shows that for WMNs the throughput decreases as O(1/n), where n is the total number of nodes in the network.
Abstract: Wireless mesh networks are an alternative technology for last-mile broadband Internet access. In WMNs, similar to ad hoc networks, each user node operates not only as a host but also as a router; user packets are forwarded to and from an Internet-connected gateway in multihop fashion. The meshed topology provides good reliability, market coverage, and scalability, as well as low upfront investments. Despite the recent startup surge in WMNs, much research remains to be done before WMNs realize their full potential. This article tackles the problem of determining the exact capacity of a WMN. The key concept we introduce to enable this calculation is the bottleneck collision domain, defined as the geographical area of the network that bounds from above the amount of data that can be transmitted in the network. We show that for WMNs the throughput of each node decreases as O(1/n), where n is the total number of nodes in the network. In contrast with most existing work on ad hoc network capacity, we do not limit our study to the asymptotic case. In particular, for a given topology and the set of active nodes, we provide exact upper bounds on the throughput of any node. The calculation can be used to provision the network, to ensure quality of service and fairness. The theoretical results are validated by detailed simulations.
TL;DR: In this article, the roles of risk, uncertainty and learning in the adoption of new technologies are reviewed, with a focus on agricultural technologies, and a conceptual framework that captures the main impacts and role of risk is outlined.
TL;DR: In this article, the relative importance of wait expectations and store atmosphere evaluations on patronage intentions was found to be critical antecedents of store patronage intentions in the context of the service-intensive retail store at which the model was tested.
31 Oct 2003
TL;DR: The analysis in this paper indicates that two pairwise key predistribution schemes can achieve better performance if such location information is available and that the smaller the deployment error is, the better performance they can achieve.
Abstract: Sensor networks are ideal candidates for applications such as target tracking and environment monitoring. Security in sensor networks is critical when there are potential adversaries. Establishment of pairwise keys is a fundamental security service, which forms the basis of other security services such as authentication and encryption. However, establishing pairwise keys in sensor networks is not a trivial task, particularly due to the resource constraints on sensors. This paper presents several techniques for establishing pairwise keys in static sensor networks. These techniques take advantage of the observation that in static sensor networks, although it is difficult to precisely pinpoint sensors' positions, it is often possible to approximately determine their locations. This paper presents a simple location-aware deployment model, and develops two pairwise key predistribution schemes, a closest pairwise keys predistribution scheme and a location-based pairwise keys scheme using bivariate polynomials, by taking advantage of sensors' expected locations. The analysis in this paper indicates that these schemes can achieve better performance if such location information is available and that the smaller the deployment error (i.e., the difference between a sensor's actual location and its expected location) is, the better performance they can achieve.
TL;DR: Older adults' memory performance across experimental conditions was observed to covary with degree of activation of the negative aging stereotype, providing support for the hypothesized relationship between stereotype activation and performance.
Abstract: This study investigated the hypothesis that age differences in memory performance may be influenced by stereotype threat associated with negative cultural beliefs about the impact of aging on memory. Recall was examined in 48 young and 48 older adults under conditions varying in the degree of induced threat. Conditions that maximize threat resulted in lower performance in older adults relative to both younger adults and to older adults who did not experience threat. The degree to which threat affected older adults’ performance increased along with the value that these individuals placed on their memory ability. Older adults’ memory performance across experimental conditions was observed to covary with degree of activation of the negative aging stereotype, providing support for the hypothesized relationship between stereotype activation and performance. Finally, stereotype threat also influenced mnemonic strategy use, which in turn partially mediated the impact of threat on recall. These results emphasize the important role played by contextual factors in determining age differences in memory performance.
TL;DR: In this paper, the authors partially sequenced over 5100 random T. reesei cDNA clones and found that most of the genes encoding known and putative biomass-degrading enzymes were transcriptionally co-regulated.
TL;DR: Comparison of diversity in equivalent samples of inbreds and open-pollinated landraces revealed that maize in breds capture <80% of the alleles in the landrace, suggesting that landraced animals can provide additional genetic diversity for maize breeding.
Abstract: Two hundred and sixty maize inbred lines, representative of the genetic diversity among essentially all public lines of importance to temperate breeding and many important tropical and subtropical lines, were assayed for polymorphism at 94 microsatellite loci. The 2039 alleles identified served as raw data for estimating genetic structure and diversity. A model-based clustering analysis placed the inbred lines in five clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. A "phylogenetic" tree was constructed to further assess the genetic structure of maize inbreds, showing good agreement with the pedigree information and the cluster analysis. Tropical and subtropical inbreds possess a greater number of alleles and greater gene diversity than their temperate counterparts. The temperate Stiff Stalk lines are on average the most divergent from all other inbred groups. Comparison of diversity in equivalent samples of inbreds and open-pollinated landraces revealed that maize inbreds capture <80% of the alleles in the landraces, suggesting that landraces can provide additional genetic diversity for maize breeding. The contributions of four different segments of the landrace gene pool to each inbred group's gene pool were estimated using a novel likelihood-based model. The estimates are largely consistent with known histories of the inbreds and indicate that tropical highland germplasm is poorly represented in maize inbreds. Core sets of inbreds that capture maximal allelic richness were defined. These or similar core sets can be used for a variety of genetic applications in maize.
TL;DR: Microarrays can survey genome-wide expression patterns and be used to identify a few genes of interest, now being creatively applied for hypothesis generation and testing.
Abstract: Microarrays are used to survey the expression of thousands of genes in a single experiment. Applied creatively, they can be used to test as well as generate new hypotheses. As the technology becomes more accessible, microarray analysis is finding applications in diverse areas of biology. Microarrays are simply a method for visualizing which genes are likely to be used in a particular tissue at a particular time under a particular set of conditions. The output of a microarray experiment is called a “gene expression profile.”
20 Mar 2003
TL;DR: The proposed solution features minimal complexity in network bandwidth, storage and processing and can achieve good accuracy, and also provides tight, deterministic bounds on both the offsets and clock drifts.
Abstract: Time synchronization is important for any distributed system. In particular, wireless sensor networks make extensive use of synchronized time in many contexts (e.g. for data fusion, TDMA schedules, synchronized sleep periods, etc.). Existing time synchronization methods were not designed with wireless sensors in mind, and need to be extended or redesigned. Our solution centers around the development of a deterministic time synchronization method relevant for wireless sensor networks. The proposed solution features minimal complexity in network bandwidth, storage and processing and can achieve good accuracy. Highly relevant for sensor networks, it also provides tight, deterministic bounds on both the offsets and clock drifts. A method to synchronize the entire network in preparation for data fusion is presented. A real implementation of a wireless ad-hoc network is used to evaluate the performance of the proposed approach.