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Showing papers by "University of California, Davis published in 2003"


Journal ArticleDOI
TL;DR: This work proposes a fully functional identity-based encryption (IBE) scheme based on bilinear maps between groups and gives precise definitions for secure IBE schemes and gives several applications for such systems.
Abstract: We propose a fully functional identity-based encryption (IBE) scheme. The scheme has chosen ciphertext security in the random oracle model assuming a variant of the computational Diffie--Hellman problem. Our system is based on bilinear maps between groups. The Weil pairing on elliptic curves is an example of such a map. We give precise definitions for secure IBE schemes and give several applications for such systems.

5,110 citations


Journal ArticleDOI
15 Aug 2003-Science
TL;DR: International integration of management strategies that support reef resilience need to be vigorously implemented, and complemented by strong policy decisions to reduce the rate of global warming.
Abstract: The diversity, frequency, and scale of human impacts on coral reefs are increasing to the extent that reefs are threatened globally. Projected increases in carbon dioxide and temperature over the next 50 years exceed the conditions under which coral reefs have flourished over the past half-million years. However, reefs will change rather than disappear entirely, with some species already showing far greater tolerance to climate change and coral bleaching than others. International integration of management strategies that support reef resilience need to be vigorously implemented, and complemented by strong policy decisions to reduce the rate of global warming.

3,664 citations


Book
01 Jan 2003
TL;DR: In this paper, the authors construct a provocative theory on the selection of leaders and present specific formal models from which their central claims can be deduced, showing how political leaders allocate resources and how institutions for selecting leaders create incentives for leaders to pursue good and bad public policy.
Abstract: The authors of this ambitious book address a fundamental political question: why are leaders who produce peace and prosperity turned out of office while those who preside over corruption, war, and misery endure? Considering this political puzzle, they also answer the related economic question of why some countries experience successful economic development and others do not. The authors construct a provocative theory on the selection of leaders and present specific formal models from which their central claims can be deduced. They show how political leaders allocate resources and how institutions for selecting leaders create incentives for leaders to pursue good and bad public policy. They also extend the model to explain the consequences of war on political survival. Throughout the book, they provide illustrations from history, ranging from ancient Sparta to Vichy France, and test the model against statistics gathered from cross-national data. The authors explain the political intuition underlying their theory in nontechnical language, reserving formal proofs for chapter appendixes. They conclude by presenting policy prescriptions based on what has been demonstrated theoretically and empirically.

3,570 citations


Journal ArticleDOI
TL;DR: In this paper, the role of facilitation in the organization of terrestrial and aquatic communities has been investigated, and the importance of a wide variety of facilitative interactions has been considered.
Abstract: Investigations of the role of competition, predation and abiotic stress in shaping natural communities were a staple for previous generations of ecologists and are still popular themes. However, more recent experimental research has uncovered the largely unanticipated, yet striking influence of facilitation (i.e. positive species interactions) on the organization of terrestrial and aquatic communities. Modern ecological concepts and theories were well established a decade before the current renaissance of interest in facilitation began, and thus do not consider the importance of a wide variety of facilitative interactions. It is time to bring ecological theory up to date by including facilitation. This process will not be painless because it will fundamentally change many basic predictions and will challenge some of our most cherished paradigms. But, ultimately, revising ecological theory will lead to a more accurate and inclusive understanding of natural communities.

2,595 citations


Journal ArticleDOI
TL;DR: The collection of case studies suggests that individual specialization is a widespread but underappreciated phenomenon that poses many important but unanswered questions.
Abstract: Most empirical and theoretical studies of resource use and population dynamics treat conspecific individuals as ecologically equivalent. This simplification is only justified if interindividual niche variation is rare, weak, or has a trivial effect on ecological processes. This article reviews the incidence, degree, causes, and implications of individual-level niche variation to challenge these simplifications. Evidence for individual specialization is available for 93 species dis- tributed across a broad range of taxonomic groups. Although few studies have quantified the degree to which individuals are specialized relative to their population, between-individual variation can some- times comprise the majority of the population's niche width. The degree of individual specialization varies widely among species and among populations, reflecting a diverse array of physiological, be- havioral, and ecological mechanisms that can generate intrapopu- lation variation. Finally, individual specialization has potentially im- portant ecological, evolutionary, and conservation implications. Theory suggests that niche variation facilitates frequency-dependent interactions that can profoundly affect the population's stability, the amount of intraspecific competition, fitness-function shapes, and the population's capacity to diversify and speciate rapidly. Our collection of case studies suggests that individual specialization is a widespread but underappreciated phenomenon that poses many important but unanswered questions.

2,391 citations


Journal ArticleDOI
TL;DR: Early mortality after VTE is strongly associated with presentation as PE, advanced age, cancer, and underlying cardiovascular disease, with a significantly higher incidence among Caucasians and African Americans than among Hispanic persons and Asian‐ Pacific Islanders.
Abstract: Venous thromboembolism (VTE) is categorized by the U.S. Surgeon General as a major public health problem. VTE is relatively common and associated with reduced survival and substantial health-care costs, and recurs frequently. VTE is a complex (multifactorial) disease, involving interactions between acquired or inherited predispositions to thrombosis and VTE risk factors, including increasing patient age and obesity, hospitalization for surgery or acute illness, nursing-home confinement, active cancer, trauma or fracture, immobility or leg paresis, superficial vein thrombosis, and, in women, pregnancy and puerperium, oral contraception, and hormone therapy. Although independent VTE risk factors and predictors of VTE recurrence have been identified, and effective primary and secondary prophylaxis is available, the occurrence of VTE seems to be relatively constant, or even increasing.

1,890 citations


Journal ArticleDOI
TL;DR: Evidence for the structural promiscuity of AhR ligand binding is described and the current state of knowledge with regards to the activation of the AhR signaling pathway by naturally occurring exogenous and endogenous ligands is discussed.
Abstract: The induction of expression of genes for xenobiotic metabolizing enzymes in response to chemical insult is an adaptive response found in most organisms. In vertebrates, the AhR is one of several chemical/ligand-dependent intracellular receptors that can stimulate gene transcription in response to xenobiotics. The ability of the AhR to bind and be activated by a range of structurally divergent chemicals suggests that the AhR contains a rather promiscuous ligand binding site. In addition to synthetic and environmental chemicals, numerous naturally occurring dietary and endogenous AhR ligands have also been identified. In this review, we describe evidence for the structural promiscuity of AhR ligand binding and discuss the current state of knowledge with regards to the activation of the AhR signaling pathway by naturally occurring exogenous and endogenous ligands.

1,716 citations


Journal ArticleDOI
TL;DR: R8s version 1.5 is a program which uses parametric, nonparametric and semiparametric methods to relax the assumption of constant rates of evolution to obtain better estimates of rates and times.
Abstract: Summary Estimating divergence times and rates of substitution from sequence data is plagued by the problem of rate variation between lineages. R8s version 1.5 is a program which uses parametric, nonparametric and semiparametric methods to relax the assumption of constant rates of evolution to obtain better estimates of rates and times. Unlike most programs for rate inference or phylogenetics, r8s permits users to convert results to absolute rates and ages by constraining one or more node times to be fixed, minimum or maximum ages (using fossil or other evidence). Version 1.5 uses truncated Newton nonlinear optimization code with bound constraints, offering superior performance over previous versions. Availability The linux executable, C source code, sample data sets and user manual are available free at http://ginger.ucdavis.edu/r8s.

1,689 citations


Journal ArticleDOI
TL;DR: In this paper, Shaver et al. focus mainly on the different attachment-related strategies of affect regulation that result from different patterns of interactions with significant others and elaborate the dynamics and functioning of these affect-regulation strategies using a recent integrative model of attachment-system activation and dynamics.
Abstract: Attachment theory (J. Bowlby, 1982/1969, 1973) is one of the most useful and generative frameworks for understanding both normative and individual-differences aspects of the process of affect regulation. In this article we focus mainly on the different attachment-related strategies of affect regulation that result from different patterns of interactions with significant others. Specifically, we pursue 3 main goals: First, we elaborate the dynamics and functioning of these affect-regulation strategies using a recent integrative model of attachment-system activation and dynamics (P. R. Shaver & M. Mikulincer, 2002). Second, we review recent findings concerning the cognitive consequences of attachment-related strategies following the arousal of positive and negative affect. Third, we propose some integrative ideas concerning the formation and development of the different attachment-related strategies.

1,583 citations


Journal ArticleDOI
TL;DR: This paper links the misunderstandings between engineers, technicians, and assemblers on a production floor to their work contexts, and demonstrates how members of these communities overcome such problems by cocreating common ground that transforms their understanding of the product and the production process.
Abstract: This paper suggests that knowledge is shared in organizations through the transformation of occupational communities' situated understandings of their work. In this paper, I link the misunderstandings between engineers, technicians, and assemblers on a production floor to their work contexts, and demonstrate how members of these communities overcome such problems by cocreating common ground that transforms their understanding of the product and the production process. In particular, I find that the communities' knowledge-sharing difficulties are rooted in differences in their language, the locus of their practice, and their conceptualization of the product. When communication problems arise, if members of these communities provide solutions which invoke the differences in the work contexts and create common ground between the communities, they can transform the understandings of others and generate a richer understanding of the product and the problems they face.

1,582 citations


Journal ArticleDOI
TL;DR: A quantized maximum signal-to-noise ratio (SNR) beamforming technique is proposed where the receiver only sends the label of the best beamforming vector in a predetermined codebook to the transmitter.
Abstract: Transmit beamforming and receive combining are simple methods for exploiting the significant diversity that is available in multiple-input multiple-output (MIMO) wireless systems. Unfortunately, optimal performance requires either complete channel knowledge or knowledge of the optimal beamforming vector; both are hard to realize. In this article, a quantized maximum signal-to-noise ratio (SNR) beamforming technique is proposed where the receiver only sends the label of the best beamforming vector in a predetermined codebook to the transmitter. By using the distribution of the optimal beamforming vector in independent and identically distributed Rayleigh fading matrix channels, the codebook design problem is solved and related to the problem of Grassmannian line packing. The proposed design criterion is flexible enough to allow for side constraints on the codebook vectors. Bounds on the codebook size are derived to guarantee full diversity order. Results on the density of Grassmannian line packings are derived and used to develop bounds on the codebook size given a capacity or SNR loss. Monte Carlo simulations are presented that compare the probability of error for different quantization strategies.

Journal ArticleDOI
TL;DR: It is shown that an important asymmetry between altruistic cooperation and altruistic punishment allows altruistic punished to evolve in populations engaged in one-time, anonymous interactions, and this process allows both altruism punishment and altruism cooperation to be maintained even when groups are large.
Abstract: Both laboratory and field data suggest that people punish noncooperators even in one-shot interactions. Although such “altruistic punishment” may explain the high levels of cooperation in human societies, it creates an evolutionary puzzle: existing models suggest that altruistic cooperation among nonrelatives is evolutionarily stable only in small groups. Thus, applying such models to the evolution of altruistic punishment leads to the prediction that people will not incur costs to punish others to provide benefits to large groups of nonrelatives. However, here we show that an important asymmetry between altruistic cooperation and altruistic punishment allows altruistic punishment to evolve in populations engaged in one-time, anonymous interactions. This process allows both altruistic punishment and altruistic cooperation to be maintained even when groups are large and other parameter values approximate conditions that characterize cultural evolution in the small-scale societies in which humans lived for most of our prehistory.

Journal ArticleDOI
TL;DR: The observed diversity of these NBS-LRR proteins indicates the variety of recognition molecules available in an individual genotype to detect diverse biotic challenges.
Abstract: The Arabidopsis genome contains ∼200 genes that encode proteins with similarity to the nucleotide binding site and other domains characteristic of plant resistance proteins. Through a reiterative process of sequence analysis and reannotation, we identified 149 NBS-LRR–encoding genes in the Arabidopsis (ecotype Columbia) genomic sequence. Fifty-six of these genes were corrected from earlier annotations. At least 12 are predicted to be pseudogenes. As described previously, two distinct groups of sequences were identified: those that encoded an N-terminal domain with Toll/Interleukin-1 Receptor homology (TIR-NBS-LRR, or TNL), and those that encoded an N-terminal coiled-coil motif (CC-NBS-LRR, or CNL). The encoded proteins are distinct from the 58 predicted adapter proteins in the previously described TIR-X, TIR-NBS, and CC-NBS groups. Classification based on protein domains, intron positions, sequence conservation, and genome distribution defined four subgroups of CNL proteins, eight subgroups of TNL proteins, and a pair of divergent NL proteins that lack a defined N-terminal motif. CNL proteins generally were encoded in single exons, although two subclasses were identified that contained introns in unique positions. TNL proteins were encoded in modular exons, with conserved intron positions separating distinct protein domains. Conserved motifs were identified in the LRRs of both CNL and TNL proteins. In contrast to CNL proteins, TNL proteins contained large and variable C-terminal domains. The extant distribution and diversity of the NBS-LRR sequences has been generated by extensive duplication and ectopic rearrangements that involved segmental duplications as well as microscale events. The observed diversity of these NBS-LRR proteins indicates the variety of recognition molecules available in an individual genotype to detect diverse biotic challenges.

Journal ArticleDOI
TL;DR: It is suggested that adiponectin concentrations are determined by intra-abdominal fat mass, with additional independent effects of age and sex, and could link intra- abdominalFat with insulin resistance and an atherogenic lipoprotein profile.
Abstract: Aims/hypothesis Increased intra-abdominal fat is associated with insulin resistance and an atherogenic lipoprotein profile. Circulating concentrations of adiponectin, an adipocyte-derived protein, are decreased with insulin resistance. We investigated the relationships between adiponectin and leptin, body fat distribution, insulin sensitivity and lipoproteins.

Book ChapterDOI
TL;DR: In this article, the authors introduce the basic concepts in Bowlby's attachment theory, covering both the normative aspects of the attachment behavioral system and individual differences, and present an integrative model of attachment-system dynamics in adulthood.
Abstract: Publisher Summary This chapter introduces the basic concepts in Bowlby's attachment theory, covering both the normative aspects of the attachment behavioral system and individual differences. It presents an integrative model of attachment-system dynamics in adulthood. The attachment system is an inborn regulatory device that has important implications for personality and interpersonal behavior. The model describes the goals of each attachment strategy and their psychological manifestations and consequences. The chapter introduces major individual differences in the functioning of the attachment system. It presents a theoretical framework that makes sense of the cognitive operations and dynamic processes involved in the activation and functioning of the attachment system in adulthood. For this, a control-system model is proposed that integrates recent findings with earlier theoretical proposals by Bowlby. The chapter summarizes the diverse empirical studies motivated by the attachment theory and reviews a variety of unresolved conceptual and empirical issues that provide an agenda for future research.

Journal ArticleDOI
TL;DR: VLSM maps for measures of speech fluency and language comprehension in 101 left-hemisphere-damaged aphasic patients confirm the anticipated contrast between anterior and posterior areas and indicate that interacting regions facilitate Fluency and auditory comprehension, in agreement with findings from modern brain imaging.
Abstract: For more than a century, lesion–symptom mapping studies have yielded valuable insights into the relationships between brain and behavior, but newer imaging techniques have surpassed lesion analysis in examining functional networks. Here we used a new method—voxel-based lesion–symptom mapping (VLSM)—to analyze the relationship between tissue damage and behavior on a voxel-by-voxel basis, as in functional neuroimaging. We applied VLSM to measures of speech fluency and language comprehension in 101 left-hemisphere-damaged aphasic patients: the VLSM maps for these measures confirm the anticipated contrast between anterior and posterior areas, and they also indicate that interacting regions facilitate fluency and auditory comprehension, in agreement with findings from modern brain imaging.

Journal ArticleDOI
TL;DR: An international consortium called `Phaseomics' is formed to establish the necessary framework of knowledge and materials that will result in disease-resistant, stress-tolerant, high-quality protein and high-yielding beans, which will be instrumental in improving living conditions in deprived regions of Africa and the Americas.
Abstract: Globally, 800 million people are malnourished. Heavily subsidised farmers in rich countries produce sufficient surplus food to feed the hungry, but not at a price the poor can afford. Even donating the rich world's surplus to the poor would not solve the problem. Most poor people earn their living from agriculture, so a deluge of free food would destroy their livelihoods. Thus, the only answer to world hunger is to safeguard and improve the productivity of farmers in poor countries. Diets of subsistence level farmers in Africa and Latin America often contain sufficient carbohydrates (through cassava, corn/maize, rice, wheat, etc.), but are poor in proteins. Dietary proteins can take the form of scarce animal products (eggs, milk, meat, etc.), but are usually derived from legumes (plants of the bean and pea family). Legumes are vital in agriculture as they form associations with bacteria that `fix-nitrogen' from the air. Effectively this amounts to internal fertilisation and is the main reason that legumes are richer in proteins than all other plants. Thousands of legume species exist but more common beans (Phaseolus vulgaris L.) are eaten than any other. In some countries such as Mexico and Brazil, beans are the primary source of protein in human diets. As half the grain legumes consumed worldwide are common beans, they represent the species of choice for the study of grain legume nutrition. Unfortunately, the yields of common beans are low even by the standards of legumes, and the quality of their seed proteins is sub-optimal. Most probably this results from millennia of selection for stable rather than high yield, and as such, is a problem that can be redressed by modern genetic techniques. We have formed an international consortium called `Phaseomics' to establish the necessary framework of knowledge and materials that will result in disease-resistant, stress-tolerant, high-quality protein and high-yielding beans. Phaseomics will be instrumental in improving living conditions in deprived regions of Africa and the Americas. It will contribute to social equity and sustainable development and enhance inter- and intra-cultural understanding, knowledge and relationships. A major goal of Phaseomics is to generate new common bean varieties that are not only suitable for but also desired by the local farmer and consumer communities. Therefore, the socio-economic dimension of improved bean production and the analysis of factors influencing the acceptance of novel varieties will be an integral part of the proposed research (see Figure 1). Here, we give an overview of the economic and nutritional importance of common beans as a food crop. Priorities and targets of current breeding programmes are outlined, along with ongoing efforts in genomics. Recommendations for an international coordinated effort to join knowledge, facilities and expertise in a variety of scientific undertakings that will contribute to the overall goal of better beans are given. To be rapid and effective, plant breeding programmes (i.e., those that involve crossing two different `parents') rely heavily on molecular `markers'. These genetic landmarks are used to position

Journal ArticleDOI
TL;DR: The results suggest that AP1 is a better candidate for VRN1 than AGLG1, and the epistatic interactions between vernalization genesVRN1 and VRN2 suggested a model in whichVRN2 would repress directly or indirectly the expression of AP1.
Abstract: Winter wheats require several weeks at low temperature to flower. This process, vernalization, is controlled mainly by the VRN1 gene. Using 6,190 gametes, we found VRN1 to be completely linked to MADS-box genes AP1 and AGLG1 in a 0.03-centimorgan interval flanked by genes Cysteine and Cytochrome B5. No additional genes were found between the last two genes in the 324-kb Triticum monococcum sequence or in the colinear regions in rice and sorghum. Wheat AP1 and AGLG1 genes were similar to Arabidopsis meristem identity genes AP1 and AGL2, respectively. AP1 transcription was regulated by vernalization in both apices and leaves, and the progressive increase of AP1 transcription was consistent with the progressive effect of vernalization on flowering time. Vernalization was required for AP1 transcription in apices and leaves in winter wheat but not in spring wheat. AGLG1 transcripts were detected during spike differentiation but not in vernalized apices or leaves, suggesting that AP1 acts upstream of AGLG1. No differences were detected between genotypes with different VRN1 alleles in the AP1 and AGLG1 coding regions, but three independent deletions were found in the promoter region of AP1. These results suggest that AP1 is a better candidate for VRN1 than AGLG1. The epistatic interactions between vernalization genes VRN1 and VRN2 suggested a model in which VRN2 would repress directly or indirectly the expression of AP1. A mutation in the promoter region of AP1 would result in the lack of recognition of the repressor and in a dominant spring growth habit.

Journal ArticleDOI
TL;DR: The theory behind alternative stable states is reviewed and to what extent these perspectives are the same, and in what ways they differ, the concepts of resilience and hysteresis, and the role of stochasticity are discussed.
Abstract: The idea that alternative stable states may exist in communities has been a recurring theme in ecology since the late 1960s, and is now experiencing a resurgence of interest. Since the first papers on the subject appeared, two perspectives have developed to describe how communities shift from one stable state to another. One assumes a constant environment with shifts in variables such as population density, and the other anticipates changes to underlying parameters or environmental “drivers”. We review the theory behind alternative stable states and examine to what extent these perspectives are the same, and in what ways they differ. We discuss the concepts of resilience and hysteresis, and the role of stochasticity within the two formulations. In spite of differences in the two perspectives, the same type of experimental evidence is required to demonstrate the existence of alternative stable states.

Journal ArticleDOI
TL;DR: Based on complementary vascular and leaf phenotypes of class III HD-ZIP and KANADI mutants, it is proposed that a common genetic program dependent upon miRNAs governs adaxial-abaxial patterning of leaves and radial patterned stems in the angiosperm shoot.

Journal ArticleDOI
TL;DR: The application of Grassmannian frames to wireless communication and to multiple description coding is discussed and their connection to unit norm tight frames for frames which are generated by group-like unitary systems is discussed.

Journal ArticleDOI
TL;DR: In this paper, the decoupling limit of the most general CP-conserving two-Higgs-doublet model was studied, where the mass of the lightest Higgs scalar is significantly smaller than the masses of the other Higgs bosons of the model.
Abstract: A CP-even neutral Higgs boson with standard-model-like couplings may be the lightest scalar of a two-Higgs-doublet model. We study the decoupling limit of the most general CP-conserving two-Higgs-doublet model, where the mass of the lightest Higgs scalar is significantly smaller than the masses of the other Higgs bosons of the model. In this case, the properties of the lightest Higgs boson are nearly indistinguishable from those of the standard model Higgs boson. The first nontrivial corrections to Higgs boson couplings in the approach to the decoupling limit are also evaluated. The importance of detecting such deviations in precision Higgs boson measurements at future colliders is emphasized. We also clarify the case in which a neutral Higgs boson can possess standard-model-like couplings in a regime where the decoupling limit does not apply. The two-Higgs-doublet sector of the minimal supersymmetric model illustrates many of the above features.

Journal ArticleDOI
TL;DR: This work fabricated fully dense nanocomposites of single-wall carbon nanotubes with nanocrystalline alumina (Al2O3) matrix at sintering temperatures as low as 1,150 °C by spark-plasma sintered, demonstrating their potential use in reinforcing nanocrystaline ceramics.
Abstract: The extraordinary mechanical, thermal and electrical properties of carbon nanotubes have prompted intense research into a wide range of applications in structural materials, electronics, chemical processing and energy management. Attempts have been made to develop advanced engineering materials with improved or novel properties through the incorporation of carbon nanotubes in selected matrices (polymers, metals and ceramics). But the use of carbon nanotubes to reinforce ceramic composites has not been very successful; for example, in alumina-based systems only a 24% increase in toughness has been obtained so far. Here we demonstrate their potential use in reinforcing nanocrystalline ceramics. We have fabricated fully dense nanocomposites of single-wall carbon nanotubes with nanocrystalline alumina (Al2O3) matrix at sintering temperatures as low as 1,150 degrees C by spark-plasma sintering. A fracture toughness of 9.7 MPa m 1/2, nearly three times that of pure nanocrystalline alumina, can be achieved.

Journal ArticleDOI
TL;DR: Computer simulation is used to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony boot strap proportion (MP-BP).
Abstract: Bayesian Markov chain Monte Carlo sampling has become increasingly popular in phylogenetics as a method for both estimating the maximum likelihood topology and for assessing nodal confidence. Despite the growing use of posterior probabilities, the relationship between the Bayesian measure of confidence and the most commonly used confidence measure in phylogenetics, the nonparametric bootstrap proportion, is poorly understood. We used computer simulation to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony bootstrap proportion (MP-BP). We simulated the evolution of DNA sequence on 17-taxon topologies under 18 evolutionary scenarios and examined the performance of these methods in assigning confidence to correct monophyletic and incorrect monophyletic groups, and we examined the effects of increasing character number on support value. BMCMC-PP and ML-BP were often strongly correlated with one another but could provide substantially different estimates of support on short internodes. In contrast, BMCMC-PP correlated poorly with MP-BP across most of the simulation conditions that we examined. For a given threshold value, more correct monophyletic groups were supported by BMCMC-PP than by either ML-BP or MP-BP. When threshold values were chosen that fixed the rate of accepting incorrect monophyletic relationship as true at 5%, all three methods recovered most of the correct relationships on the simulated topologies, although BMCMC-PP and ML-BP performed better than MP-BP. BMCMC-PP was usually a less biased predictor of phylogenetic accuracy than either bootstrapping method. BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap.

Journal ArticleDOI
TL;DR: In this article, the authors investigated the impact of various agricultural practices on levels of secondary plant metabolites, and found that higher levels of TPs were consistently found in organically and sustainably grown foods as compared to those produced by conventional agricultural practices.
Abstract: Secondary phenolic metabolites play an important role in plant defense mechanisms, and increasing evidence indicates that many are important in human health. To date, few studies have investigated the impact of various agricultural practices on levels of secondary plant metabolites. To address this issue, the total phenolic (TP) content of marionberries, strawberries, and corn grown by sustainable, organic, or conventional cultural practices were measured. Additionally, the effects of three common postharvest processing treatments (freezing, freeze-drying, and air-drying) on the TP content of these agricultural products were also investigated. Statistically higher levels of TPs were consistently found in organically and sustainably grown foods as compared to those produced by conventional agricultural practices. In all samples, freeze-drying preserved higher levels of TPs in comparison with air-drying.

Journal ArticleDOI
TL;DR: The evolving IL-17 family of ligands and receptors may play an important role in the homeostasis of tissues in health and disease beyond the immune system, as reviewed in this survey.

Journal ArticleDOI
TL;DR: In this paper, the authors examined different approaches to protect a mesh-based WDM optical network from such failures and proposed distributed protocols for path and link restoration, and formulated a model of protection-switching times for different protection schemes based on a fully distributed control network.
Abstract: In a wavelength-division-multiplexing (WDM) optical network, the failure of network elements (e.g., fiber links and cross connects) may cause the failure of several optical channels, thereby leading to large data losses. This study examines different approaches to protect a mesh-based WDM optical network from such failures. These approaches are based on two survivability paradigms: 1) path protection/restoration and 2) link protection/restoration. The study examines the wavelength capacity requirements, and routing and wavelength assignment of primary and backup paths for path and link protection and proposes distributed protocols for path and link restoration. The study also examines the protection-switching time and the restoration time for each of these schemes, and the susceptibility of these schemes to multiple link failures. The numerical results obtained for a representative network topology with random traffic demands demonstrate that there is a tradeoff between the capacity utilization and the susceptibility to multiple link failures. We find that, on one hand, path protection provides significant capacity savings over link protection, and shared protection provides significant savings over dedicated protection; while on the other hand, path protection is more susceptible to multiple link failures than link protection, and shared protection is more susceptible to multiple link failures than dedicated protection. We formulate a model of protection-switching times for the different protection schemes based on a fully distributed control network. We propose distributed control protocols for path and link restoration. Numerical results obtained by simulating these protocols indicate that, for a representative network topology, path restoration has a better restoration efficiency than link restoration, and link restoration has a faster restoration time compared with path restoration.

Journal ArticleDOI
TL;DR: It is demonstrated that near-complete restoration of mucosal immune system can be achieved by initiating HAART early in HIV-1 infection and monitoring of the restoration and/or maintenance of CD4+ T cells in GALT provides a more accurate assessment of the efficacy of antiviral host immune responses as well as HAART.
Abstract: Gut-associated lymphoid tissue (GALT) harbors the majority of T lymphocytes in the body and is an important target for human immunodeficiency virus type 1 (HIV-1). We analyzed longitudinal jejunal biopsy samples from HIV-1-infected patients, during both primary and chronic stages of HIV-1 infection, prior to and following the initiation of highly active antiretroviral therapy (HAART) to determine the onset of CD4 + T-cell depletion and the effect of HAART on the restoration of CD4 + T cells in GALT. Severe depletion of intestinal CD4 + T cells occurred during primary HIV-1 infection. Our results showed that the restoration of intestinal CD4 + T cells following HAART in chronically HIV-1-infected patients was substantially delayed and incomplete. In contrast, initiation of HAART during early stages of infection resulted in near-complete restoration of intestinal CD4 + T cells, despite the delay in comparison to peripheral blood CD4 + T-cell recovery. DNA microarray analysis of gene expression profiles and flow-cytometric analysis of lymphocyte homing and cell proliferation markers demonstrated that cell trafficking to GALT and not local proliferation contributed to CD4 + T-cell restoration. Evaluation of jejunal biopsy samples from long-term HIV-1-infected nonprogressors showed maintenance of normal CD4 + T-cell levels in both GALT and peripheral blood. Our results demonstrate that near-complete restoration of mucosal immune system can be achieved by initiating HAART early in HIV-1 infection. Monitoring of the restoration and/or maintenance of CD4 + T cells in GALT provides a more accurate assessment of the efficacy of antiviral host immune responses as well as HAART.


Journal ArticleDOI
TL;DR: The fabrication methods and physical properties of ordered magnetic nanostructures with dimensions on the submicron to nanometer scale are reviewed in this article, where various types of nanofabrication techniques are described, and their capabilities and limitations in achieving magnetic nano-structures are discussed.