Showing papers by "North Carolina State University published in 2005"

A haplotype map of the human genome

Abstract: Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.

PowerMarker: an integrated analysis environment for genetic marker analysis

Abstract: Summary: PowerMarker delivers a data-driven, integrated analysis environment (IAE) for genetic data. The IAE integrates data management, analysis and visualization in a user-friendly graphical user interface. It accelerates the analysis lifecycle and enables users to maintain data integrity throughout the process. An ever-growing list of more than 50 different statistical analyses for genetic markers has been implemented in PowerMarker. Availability: www.powermarker.net Contact: powermarker@hotmail.com

Creating Something from Nothing: Resource Construction through Entrepreneurial Bricolage:

Abstract: A field study of 29 resource-constrained firms that varied dramatically in their responses to similar objective environments is used to examine the process by which entrepreneurs in resource-poor environments were able to render unique services by recombining elements at hand for new purposes that challenged institutional definitions and limits. We found that Levi-Strauss's concept of bricolage—making do with what is at hand—explained many of the behaviors we observed in small firms that were able to create something from nothing by exploiting physical, social, or institutional inputs that other firms rejected or ignored. We demonstrate the socially constructed nature of resource environments and the role of bricolage in this construction. Using our field data and the existing literature on bricolage, we advance a formal definition of entrepreneurial bricolage and induce the beginnings of a process model of bricolage and firm growth. Central to our contribution is the notion that companies engaging in bri...

HyPhy: hypothesis testing using phylogenies

Abstract: Summary: The HyPhypackage is designed to provide a flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies of rates and patterns of sequence evolution. Availability: http://www.hyphy.org Contact: muse@stat.ncsu.edu Supplementary information:HyPhydocumentation and tutorials are available at http://www.hyphy.org

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Abstract: Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

Principles for characterizing the potential human health effects from exposure to nanomaterials: elements of a screening strategy.

Abstract: The rapid proliferation of many different engineered nanomaterials (defined as materials designed and produced to have structural features with at least one dimension of 100 nanometers or less) presents a dilemma to regulators regarding hazard identification. The International Life Sciences Institute Research Foundation/Risk Science Institute convened an expert working group to develop a screening strategy for the hazard identification of engineered nanomaterials. The working group report presents the elements of a screening strategy rather than a detailed testing protocol. Based on an evaluation of the limited data currently available, the report presents a broad data gathering strategy applicable to this early stage in the development of a risk assessment process for

Understanding Student Differences

Abstract: Students have different levels of motivation, different attitudes about teaching and learning, and different responses to specific classroom environments and instructional practices. The more thoroughly instructors understand the differences, the better chance they have of meeting the diverse learning needs of all of their students. Three categories of diversity that have been shown to have important implications for teaching and learning are differences in students' learning styles (characteristic ways of taking in and processing information), approaches to learning (surface, deep, and strategic), and intellectual development levels (attitudes about the nature of knowledge and how it should be acquired and evaluated). This article reviews models that have been developed for each of these categories, outlines their pedagogical implications, and suggests areas for further study.

The genome sequence of the rice blast fungus Magnaporthe grisea

Abstract: Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.

Service-oriented computing

Abstract: Traditional approaches to software development - the ones embodied in CASE tools and modeling frameworks - are appropriate for building individual software components, but they are not designed to face the challenges of open environments. Service-oriented computing provides a way to create a new architecture that reflects components' trends toward autonomy and heterogeneity. We thus emphasize SOC concepts instead of how to deploy Web services in accord with current standards. To begin the series, we describe the key concepts and abstractions of SOC and the elements of a corresponding engineering methodology.

Oxidative stress: molecular perception and transduction of signals triggering antioxidant gene defenses

Abstract: Molecular oxygen (O2) is the premier biological electron acceptor that serves vital roles in fundamental cellular functions. However, with the beneficial properties of O2 comes the inadvertent formation of reactive oxygen species (ROS) such as superoxide (O2*-), hydrogen peroxide, and hydroxyl radical (OH*). If unabated, ROS pose a serious threat to or cause the death of aerobic cells. To minimize the damaging effects of ROS, aerobic organisms evolved non-enzymatic and enzymatic antioxidant defenses. The latter include catalases, peroxidases, superoxide dismutases, and glutathione S-transferases (GST). Cellular ROS-sensing mechanisms are not well understood, but a number of transcription factors that regulate the expression of antioxidant genes are well characterized in prokaryotes and in yeast. In higher eukaryotes, oxidative stress responses are more complex and modulated by several regulators. In mammalian systems, two classes of transcription factors, nuclear factor kB and activator protein-1, are involved in the oxidative stress response. Antioxidant-specific gene induction, involved in xenobiotic metabolism, is mediated by the "antioxidant responsive element" (ARE) commonly found in the promoter region of such genes. ARE is present in mammalian GST, metallothioneine-I and MnSod genes, but has not been found in plant Gst genes. However, ARE is present in the promoter region of the three maize catalase (Cat) genes. In plants, ROS have been implicated in the damaging effects of various environmental stress conditions. Many plant defense genes are activated in response to these conditions, including the three maize Cat and some of the superoxide dismutase (Sod) genes.

Z-MAC: a hybrid MAC for wireless sensor networks

Abstract: This paper presents the design, implementation and performance evaluation of a hybrid MAC protocol, called Z-MAC, for wireless sensor networks that combines the strengths of TDMA and CSMA while offsetting their weaknesses Like CSMA, Z-MAC achieves high channel utilization and low-latency under low contention and like TDMA, achieves high channel utilization under high contention and reduces collision among two-hop neighbors at a low cost A distinctive feature of Z-MAC is that its performance is robust to synchronization errors, slot assignment failures and time-varying channel conditions; in the worst case, its performance always falls back to that of CSMA Z-MAC is implemented in TinyOS

Forest response to elevated CO2 is conserved across a broad range of productivity.

Abstract: Climate change predictions derived from coupled carbon-climate models are highly dependent on assumptions about feedbacks between the biosphere and atmosphere. One critical feedback occurs if C uptake by the biosphere increases in response to the fossil-fuel driven increase in atmospheric [CO2] (“CO2 fertilization”), thereby slowing the rate of increase in atmospheric [CO2]. Carbon exchanges between the terrestrial biosphere and atmosphere are often first represented in models as net primary productivity (NPP). However, the contribution of CO2 fertilization to the future global C cycle has been uncertain, especially in forest ecosystems that dominate global NPP, and models that include a feedback between terrestrial biosphere metabolism and atmospheric [CO2] are poorly constrained by experimental evidence. We analyzed the response of NPP to elevated CO2 (≈550 ppm) in four free-air CO2 enrichment experiments in forest stands. We show that the response of forest NPP to elevated [CO2] is highly conserved across a broad range of productivity, with a stimulation at the median of 23 ± 2%. At low leaf area indices, a large portion of the response was attributable to increased light absorption, but as leaf area indices increased, the response to elevated [CO2] was wholly caused by increased light-use efficiency. The surprising consistency of response across diverse sites provides a benchmark to evaluate predictions of ecosystem and global models and allows us now to focus on unresolved questions about carbon partitioning and retention, and spatial variation in NPP response caused by availability of other growth limiting resources.

Essential function for the kinase TAK1 in innate and adaptive immune responses.

Abstract: Transforming growth factor-beta-activated kinase 1 (TAK1) has been linked to interleukin 1 receptor and tumor necrosis factor receptor signaling. Here we generated mouse strains with conditional expression of a Map3k7 allele encoding part of TAK1. TAK1-deficient embryonic fibroblasts demonstrated loss of responses to interleukin 1beta and tumor necrosis factor. Studies of mice with B cell-specific TAK1 deficiency showed that TAK1 was indispensable for cellular responses to Toll-like receptor ligands, CD40 and B cell receptor crosslinking. In addition, antigen-induced immune responses were considerably impaired in mice with B cell-specific TAK1 deficiency. TAK1-deficient cells failed to activate transcription factor NF-kappaB and mitogen-activated protein kinases in response to interleukin 1beta, tumor necrosis factor and Toll-like receptor ligands. However, TAK1-deficient B cells were able to activate NF-kappaB but not the kinase Jnk in response to B cell receptor stimulation. These results collectively indicate that TAK1 is key in the cellular response to a variety of stimuli.

Do Satisfied Customers Buy More? Examining Moderating Influences in a Retailing Context:

Abstract: In this research, the authors propose that the relationship between satisfaction and repurchase behavior is moderated by customer, relational, and marketplace characteristics. They further hypothesize that the moderating effects emerge if repurchase is measured as objective behavior but not if it is measured as repurchase intentions. To test for systematic differences in effects, the authors estimate identical models using both longitudinal repurchase measures and survey measures as the dependent variable. The results suggest that the relationship between customer satisfaction and repurchase behavior is contingent on the moderating effects of convenience, competitive intensity, customer involvement, and household income. As the authors predicted, the results are significantly different for self-reported repurchase intentions and objective repurchase behavior. The conceptual framework and empirical findings reinforce the importance of moderating influences and offer new insights that enhance the understanding of what drives repurchase behavior.

Demystifying 3D ICs: the pros and cons of going vertical

Abstract: This article provides a practical introduction to the design trade-offs of the currently available 3D IC technology options. It begins with an overview of techniques, such as wire bonding, microbumps, through vias, and contactless interconnection, comparing them in terms of vertical density and practical limits to their use. We then present a high-level discussion of the pros and cons of 3D technologies, with an analysis relating the number of transistors on a chip to the vertical interconnect density using estimates based on Rent's rule. Next, we provide a more detailed design example of inductively coupled interconnects, with measured results of a system fabricated in a 0.35-/spl mu/m technology and an analysis of misalignment and crosstalk tolerances. Lastly, we present a case study of a fast Fourier transform (FFT) placed and routed in a 0.18-/spl mu/m through-via silicon-on-insulator (SOI) technology, comparing the 3D design to a traditional 2D approach in terms of wire length and critical-path delay.

Probing BSA binding to citrate-coated gold nanoparticles and surfaces.

Abstract: The interaction of bovine serum albumin (BSA) with gold colloids and surfaces was studied using ζ-potential and quartz crystal microbalance (QCM) measurements, respectively, to determine the surface charge and coverage. The combination of these two measurements suggests that BSA binding to gold nanoparticles and gold surfaces occurs by an electrostatic mechanism when citrate is present. The binding of BSA to bare gold is nearly two times greater than the binding of BSA to a citrate-coated gold surface, suggesting that protein spreading (denaturation) on the surface may occur followed by secondary protein binding. On the other hand, binding to citrate-coated gold surfaces can be fit to a Langmuir isotherm model to obtain a maximum surface coverage of (3.7 ± 0.2) × 1012 molecules/cm2 and a binding constant of 1.0 ± 0.3 μM-1. The ζ-potential measurements show that the stabilization of colloids by BSA has a significant contribution from a steric mechanism because the colloids are stable, even at their isoelec...

Establishing pairwise keys in distributed sensor networks

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 sensor nodes, it is not feasible to use traditional key management techniques such as public key cryptography and key distribution center (KDC). A number of key predistribution techniques have been proposed for pairwise key establishment in sensor networks recently. To facilitate the study of novel pairwise key predistribution techniques, this paper develops a general framework for establishing pairwise keys between sensor nodes using bivariate polynomials. This paper then proposes two efficient instantiations of the general framework: a random subset assignment key predistribution scheme, and a hypercube-based key predistribution scheme. The analysis shows that both schemes have a number of nice properties, including high probability, or guarantee to establish pairwise keys, tolerance of node captures, and low storage, communication, and computation overhead. To further reduce the computation at sensor nodes, this paper presents an optimization technique for polynomial evaluation, which is used to compute pairwise keys. This paper also reports the implementation and the performance of the proposed schemes on MICA2 motes running TinyOS, an operating system for networked sensors. The results indicate that the proposed techniques can be applied efficiently in resource-constrained sensor networks.

Maize association population: a high-resolution platform for quantitative trait locus dissection.

Abstract: *Summary Crop improvement and the dissection of complex genetic traits require germplasm diversity. Although this necessary phenotypic variability exists in diverse maize, most research is conducted using a small subset of inbred lines. An association population of 302 lines is now available – a valuable research tool that captures a large proportion of the alleles in cultivated maize. Provided that appropriate statistical models correcting for population structure are included, this tool can be used in association analyses to provide high-resolution evaluation of multiple alleles. This study describes the population structure of the 302 lines, and investigates the relationship between population structure and various measures of phenotypic and breeding value. On average, our estimates of population structure account for 9.3% of phenotypic variation, roughly equivalent to a major quantitative trait locus (QTL), with a high of 35%. Inclusion of population structure in association models is critical to meaningful analyses. This new association population has the potential to identify QTL with small effects, which will aid in dissecting complex traits and in planning future projects to exploit the rich diversity present in maize.

Use of relative code churn measures to predict system defect density

Abstract: Software systems evolve over time due to changes in requirements, optimization of code, fixes for security and reliability bugs etc. Code churn, which measures the changes made to a component over a period of time, quantifies the extent of this change. We present a technique for early prediction of system defect density using a set of relative code churn measures that relate the amount of churn to other variables such as component size and the temporal extent of churn. Using statistical regression models, we show that while absolute measures of code chum are poor predictors of defect density, our set of relative measures of code churn is highly predictive of defect density. A case study performed on Windows Server 2003 indicates the validity of the relative code churn measures as early indicators of system defect density. Furthermore, our code churn metric suite is able to discriminate between fault and not fault-prone binaries with an accuracy of 89.0 percent.

Facile means for quantifying microRNA expression by real-time PCR

Abstract: MicroRNAs (miRNAs) are 20-24 nucleotide RNAs that are predicted to play regulatory roles in animals and plants. Here we report a simple and sensitive real-time PCR method for quantifying the expression of plant miRNAs. Total RNA, including miRNAs, was polyadenylated and reverse-transcribed with a poly(T) adapter into cDNAs for real-time PCR using the miRNA-specific forward primer and the sequence complementary to the poly(T) adapter as the reverse primer. Several Arabidopsis miRNA sequences were tested using SYBR Green reagent, demonstrating that this method, using as little as 100 pg total RNA, could readily discriminate the expression of miRNAs having asfew as one nucleotide sequence difference. This method also revealed miRNA tissue-specific expression patterns that cannot be resolved by Northern blot analysis and may therefore be widely useful for characterizing miRNA expression in plants as well as in animals.

Nested self-similar wrinkling patterns in skins.

Abstract: Stiff thin films on soft substrates are both ancient and commonplace in nature; for instance, animal skin comprises a stiff epidermis attached to a soft dermis. Although more recent and rare, artificial skins are increasingly used in a broad range of applications, including flexible electronics, tunable diffraction gratings, force spectroscopy in cells, modern metrology methods, and other devices. Here we show that model elastomeric artificial skins wrinkle in a hierarchical pattern consisting of self-similar buckles extending over five orders of magnitude in length scale, ranging from a few nanometres to a few millimetres. We provide a mechanism for the formation of this hierarchical wrinkling pattern, and quantify our experimental findings with both computations and a simple scaling theory. This allows us to harness the substrates for applications. In particular, we show how to use the multigeneration-wrinkled substrate for separating particles based on their size, while simultaneously forming linear chains of monodisperse particles.

The Contribution of Commercial Fertilizer Nutrients to Food Production

Abstract: technology and intensified production often involve a greater need for commercial fertilizer nutrients to avoid Nutrient inputs in crop production systems have come under innutrient depletion and ensure soil quality and crop procreased scrutiny in recent years because of the potential for environductivity. The need for increased inputs correctly raises mental impact from inputs such as N and P. The benefits of nutrient inputsareoftenminimizedindiscussionsofpotentialrisk.Thepurpose questions about associated risks. Potential risks are ofof this article is to examine existing data and approximate the effects ten widely publicized while the associated benefits of of nutrient inputs, specifically from commercial fertilizers, on crop an abundant, affordable, and healthful food supply can yield. Several long-term studies in the USA, England, and the tropics, be overlooked or understated. To judge any such pracalong with the results from an agricultural chemical use study and ticeorsystem,therisksmustbeevaluatedincomparison nutrient budget information, were evaluated. A total of 362 seasons with the benefits. While misuses of agricultural fertilizof crop production were included in the long-term study evaluations. ers have undoubtedly occurred and concerns about how Crops utilized in these studies included corn (Zea mays L.), wheat fertilizers affect the environment have sometimes been (Triticum aestivum L.), soybean [Glycine max (L.) Merr.], rice (Oroverstated, the purpose of this article is not to address yza sativa L.), and cowpea [Vigna unguiculata (L.) Walp.]. The these issues but to provide evidence of the impact comaverage percentage of yield attributable to fertilizer generally ranged from about 40 to 60% in the USA and England and tended to be mercial fertilizers have had on agricultural production. much higher in the tropics. Recently calculated budgets for N, P, and Several attempts have previously been made to estiKindicatethatcommercialfertilizer makesupthemajorityofnutrient mate how much of the crop production in the USA is inputs necessary to sustain current crop yields in the USA. The results attributable to commercial nutrient inputs. These estiof this investigation indicate that the commonly cited generalization mates usually range from about 30 to 50% for major that at least 30 to 50% of crop yield is attributable to commercial grain crops (Nelson, 1990). Determining these estimates fertilizer nutrient inputs is a reasonable, if not conservative estimate. presents significant challenges, and assumptions are always required regardless of the approach taken. One difficulty that arises is that crops respond differently to M

Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation

Abstract: Pollination in flowering plants requires that anthers release pollen when the gynoecium is competent to support fertilization. We show that in Arabidopsis thaliana, two paralogous auxin response transcription factors, ARF6 and ARF8, regulate both stamen and gynoecium maturation. arf6 arf8 double-null mutant flowers arrested as infertile closed buds with short petals, short stamen filaments, undehisced anthers that did not release pollen and immature gynoecia. Numerous developmentally regulated genes failed to be induced. ARF6 and ARF8 thus coordinate the transition from immature to mature fertile flowers. Jasmonic acid (JA) measurements and JA feeding experiments showed that decreased jasmonate production caused the block in pollen release, but not the gynoecium arrest. The double mutant had altered auxin responsive gene expression. However, whole flower auxin levels did not change during flower maturation, suggesting that auxin might regulate flower maturation only under specific environmental conditions, or in localized organs or tissues of flowers. arf6 and arf8 single mutants and sesquimutants (homozygous for one mutation and heterozygous for the other) had delayed stamen development and decreased fecundity, indicating that ARF6 and ARF8 gene dosage affects timing of flower maturation quantitatively.

Mechanism of Phosphorescence Appropriate for the Long-Lasting Phosphors Eu2+-Doped SrAl2O4 with Codopants Dy3+ and B3+

Abstract: The existing mechanisms proposed to explain the phosphorescence of SrAl2O4:Eu2+,Dy3+ and related phosphors were found to be inconsistent with a number of important experimental and theoretical observations. We formulated a new mechanism of phosphorescence on the basis of the facts that the d orbitals of Eu2+ are located near the conduction band bottom of SrAl2O4, that the Eu2+ concentration decreases during UV excitation, and that trace amounts of Eu3+ are always present in these phosphors. In our mechanism, some Eu2+ ions are oxidized to Eu3+ under UV, and the released electrons are trapped at the oxygen vacancy levels located in the vicinity of the photogenerated Eu3+ cations. The phosphorescence arises from the recombination of these trapped electrons around the photogenerated Eu3+ sites with emission at 520 nm. The codopant Dy3+ enhances the phosphorescence by increasing the number and the depth of electron traps, and the codopant B3+ enhances the phosphorescence by increasing the depth of electron tr...

Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis.

Abstract: MicroRNAs (miRNAs) are small, noncoding RNAs that can play crucial regulatory roles in eukaryotes by targeting mRNAs for silencing. To test whether miRNAs play roles in the regulation of wood development in tree species, we isolated small RNAs from the developing xylem of Populus trichocarpa stems and cloned 22 miRNAs. They are the founding members of 21 miRNA gene families for 48 miRNA sequences, represented by 98 loci in the Populus genome. A majority of these miRNAs were predicted to target developmental- and stress/defense-related genes and possible functions associated with the biosynthesis of cell wall metabolites. Of the 21 P. trichocarpa miRNA families, 11 have sequence conservation in Arabidopsis thaliana but exhibited species-specific developmental expression patterns, suggesting that even conserved miRNAs may have different regulatory roles in different species. Most unexpectedly, the remaining 10 miRNAs, for which 17 predicted targets were experimentally validated in vivo, are absent from the Arabidopsis genome, suggesting possible roles in tree-specific processes. In fact, the expression of a majority of the cloned miRNAs was upregulated or downregulated in woody stems in a manner consistent with tree-specific corrective growth against tension and compression stresses, two constant mechanical loads in trees. Our results show that plant miRNAs can be induced by mechanical stress and may function in one of the most critical defense systems for structural and mechanical fitness.