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Showing papers by "Oregon State University published in 2010"


Journal ArticleDOI
TL;DR: In this paper, the authors present the first global assessment of recent tree mortality attributed to drought and heat stress and identify key information gaps and scientific uncertainties that currently hinder our ability to predict tree mortality in response to climate change and emphasizes the need for a globally coordinated observation system.

5,811 citations


Journal ArticleDOI
TL;DR: This paper describes Meep, a popular free implementation of the finite-difference time-domain (FDTD) method for simulating electromagnetism, and focuses on aspects of implementing a full-featured FDTD package that go beyond standard textbook descriptions of the algorithm.

2,489 citations


Journal ArticleDOI
TL;DR: A molecular-level assessment of the physical organization and chemical complexity of biomass-derived chars and, specifically, that of aromatic carbon in char structures suggests the existence of four distinct categories of char consisting of a unique mixture of chemical phases and physical states.
Abstract: Char black carbon (BC), the solid residue of incomplete combustion, is continuously being added to soils and sediments due to natural vegetation fires, anthropogenic pollution, and new strategies for carbon sequestration (“biochar”). Here we present a molecular-level assessment of the physical organization and chemical complexity of biomass-derived chars and, specifically, that of aromatic carbon in char structures. Brunauer−Emmett−Teller (BET)−N2 surface area (SA), X-ray diffraction (XRD), synchrotron-based near-edge X-ray absorption fine structure (NEXAFS), and Fourier transform infrared (FT-IR) spectroscopy are used to show how two plant materials (wood and grass) undergo analogous but quantitatively different physical−chemical transitions as charring temperature increases from 100 to 700 °C. These changes suggest the existence of four distinct categories of char consisting of a unique mixture of chemical phases and physical states: (i) in transition chars, the crystalline character of the precursor ma...

2,283 citations


Journal ArticleDOI
TL;DR: An overview of recent progress in the area of cellulose nanofibre-based nanocomposites is given in this article, with particular emphasis on applications, such as reinforced adhesives, to make optically transparent paper for electronic displays, to create DNA-hybrid materials, to generate hierarchical composites and for use in foams, aerogels and starch nanocom composites.
Abstract: This paper provides an overview of recent progress made in the area of cellulose nanofibre-based nanocomposites. An introduction into the methods used to isolate cellulose nanofibres (nanowhiskers, nanofibrils) is given, with details of their structure. Following this, the article is split into sections dealing with processing and characterisation of cellulose nanocomposites and new developments in the area, with particular emphasis on applications. The types of cellulose nanofibres covered are those extracted from plants by acid hydrolysis (nanowhiskers), mechanical treatment and those that occur naturally (tunicate nanowhiskers) or under culturing conditions (bacterial cellulose nanofibrils). Research highlighted in the article are the use of cellulose nanowhiskers for shape memory nanocomposites, analysis of the interfacial properties of cellulose nanowhisker and nanofibril-based composites using Raman spectroscopy, switchable interfaces that mimic sea cucumbers, polymerisation from the surface of cellulose nanowhiskers by atom transfer radical polymerisation and ring opening polymerisation, and methods to analyse the dispersion of nanowhiskers. The applications and new advances covered in this review are the use of cellulose nanofibres to reinforce adhesives, to make optically transparent paper for electronic displays, to create DNA-hybrid materials, to generate hierarchical composites and for use in foams, aerogels and starch nanocomposites and the use of all-cellulose nanocomposites for enhanced coupling between matrix and fibre. A comprehensive coverage of the literature is given and some suggestions on where the field is likely to advance in the future are discussed.

2,214 citations


Journal ArticleDOI
TL;DR: Relations of traits to specific coping responses reveal a more nuanced picture and recommendations are presented for ways future research can expand on the growing understanding of how personality and coping shape adjustment to stress.
Abstract: Personality psychology addresses views of human nature and individual differences. Biological and goal-based views of human nature provide an especially useful basis for construing coping; the five-factor model of traits adds a useful set of individual differences. Coping—responses to adversity and to the distress that results—is categorized in many ways. Meta-analyses link optimism, extraversion, conscientiousness, and openness to more engagement coping; neuroticism to more disengagement coping; and optimism, conscientiousness, and agreeableness to less disengagement coping. Relations of traits to specific coping responses reveal a more nuanced picture. Several moderators of these associations also emerge: age, stressor severity, and temporal proximity between the coping activity and the coping report. Personality and coping play both independent and interactive roles in influencing physical and mental health. Recommendations are presented for ways future research can expand on the growing understanding of how personality and coping shape adjustment to stress.

1,845 citations


Journal ArticleDOI
John P. Vogel1, David F. Garvin2, Todd C. Mockler2, Jeremy Schmutz, Daniel S. Rokhsar3, Michael W. Bevan4, Kerrie Barry5, Susan Lucas5, Miranda Harmon-Smith5, Kathleen Lail5, Hope Tice5, Jane Grimwood, Neil McKenzie4, Naxin Huo6, Yong Q. Gu6, Gerard R. Lazo6, Olin D. Anderson6, Frank M. You7, Ming-Cheng Luo7, Jan Dvorak7, Jonathan M. Wright4, Melanie Febrer4, Dominika Idziak8, Robert Hasterok8, Erika Lindquist5, Mei Wang5, Samuel E. Fox2, Henry D. Priest2, Sergei A. Filichkin2, Scott A. Givan2, Douglas W. Bryant2, Jeff H. Chang2, Haiyan Wu9, Wei Wu10, An-Ping Hsia10, Patrick S. Schnable9, Anantharaman Kalyanaraman11, Brad Barbazuk12, Todd P. Michael, Samuel P. Hazen13, Jennifer N. Bragg6, Debbie Laudencia-Chingcuanco6, Yiqun Weng14, Georg Haberer, Manuel Spannagl, Klaus F. X. Mayer, Thomas Rattei15, Therese Mitros3, Sang-Jik Lee16, Jocelyn K. C. Rose16, Lukas A. Mueller16, Thomas L. York16, Thomas Wicker17, Jan P. Buchmann17, Jaakko Tanskanen18, Alan H. Schulman18, Heidrun Gundlach, Michael W. Bevan4, Antonio Costa de Oliveira19, Luciano da C. Maia19, William R. Belknap6, Ning Jiang, Jinsheng Lai9, Liucun Zhu20, Jianxin Ma20, Cheng Sun21, Ellen J. Pritham21, Jérôme Salse, Florent Murat, Michael Abrouk, Rémy Bruggmann, Joachim Messing, Noah Fahlgren2, Christopher M. Sullivan2, James C. Carrington2, Elisabeth J. Chapman, Greg D. May22, Jixian Zhai23, Matthias Ganssmann23, Sai Guna Ranjan Gurazada23, Marcelo A German23, Blake C. Meyers23, Pamela J. Green23, Ludmila Tyler3, Jiajie Wu7, James A. Thomson6, Shan Chen13, Henrik Vibe Scheller24, Jesper Harholt25, Peter Ulvskov25, Jeffrey A. Kimbrel2, Laura E. Bartley24, Peijian Cao24, Ki-Hong Jung26, Manoj Sharma24, Miguel E. Vega-Sánchez24, Pamela C. Ronald24, Chris Dardick6, Stefanie De Bodt27, Wim Verelst27, Dirk Inzé27, Maren Heese28, Arp Schnittger28, Xiaohan Yang29, Udaya C. Kalluri29, Gerald A. Tuskan29, Zhihua Hua14, Richard D. Vierstra14, Yu Cui9, Shuhong Ouyang9, Qixin Sun9, Zhiyong Liu9, Alper Yilmaz30, Erich Grotewold30, Richard Sibout31, Kian Hématy31, Grégory Mouille31, Herman Höfte31, Todd P. Michael, Jérôme Pelloux32, Devin O'Connor3, James C. Schnable3, Scott C. Rowe3, Frank G. Harmon3, Cynthia L. Cass33, John C. Sedbrook33, Mary E. Byrne4, Sean Walsh4, Janet Higgins4, Pinghua Li16, Thomas P. Brutnell16, Turgay Unver34, Hikmet Budak34, Harry Belcram, Mathieu Charles, Boulos Chalhoub, Ivan Baxter35 
11 Feb 2010-Nature
TL;DR: The high-quality genome sequence will help Brachypodium reach its potential as an important model system for developing new energy and food crops and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat.
Abstract: Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.

1,603 citations


Journal ArticleDOI
02 Dec 2010-Nature
TL;DR: Overall, despite many remaining questions, current evidence indicates that preserving intact ecosystems and their endemic biodiversity should generally reduce the prevalence of infectious diseases.
Abstract: Current unprecedented declines in biodiversity reduce the ability of ecological communities to provide many fundamental ecosystem services. Here we evaluate evidence that reduced biodiversity affects the transmission of infectious diseases of humans, other animals and plants. In principle, loss of biodiversity could either increase or decrease disease transmission. However, mounting evidence indicates that biodiversity loss frequently increases disease transmission. In contrast, areas of naturally high biodiversity may serve as a source pool for new pathogens. Overall, despite many remaining questions, current evidence indicates that preserving intact ecosystems and their endemic biodiversity should generally reduce the prevalence of infectious diseases.

1,513 citations


Journal ArticleDOI
TL;DR: Implementation of a new toxicity testing paradigm firmly based on human biology by transitioning from current expensive and lengthy in vivo testing with qualitative endpoints to in vitro toxicity pathway assays on human cells or cell lines using robotic high-throughput screening with mechanistic quantitative parameters.
Abstract: With the release of the landmark report Toxicity Testing in the 21st Century: A Vision and a Strategy, the U.S. National Academy of Sciences, in 2007, precipitated a major change in the way toxicity testing is conducted. It envisions increased efficiency in toxicity testing and decreased animal usage by transitioning from current expensive and lengthy in vivo testing with qualitative endpoints to in vitro toxicity pathway assays on human cells or cell lines using robotic high-throughput screening with mechanistic quantitative parameters. Risk assessment in the exposed human population would focus on avoiding significant perturbations in these toxicity pathways. Computational systems biology models would be implemented to determine the dose-response models of perturbations of pathway function. Extrapolation of in vitro results to in vivo human blood and tissue concentrations would be based on pharmacokinetic models for the given exposure condition. This practice would enhance human relevance of test results, and would cover several test agents, compared to traditional toxicological testing strategies. As all the tools that are necessary to implement the vision are currently available or in an advanced stage of development, the key prerequisites to achieving this paradigm shift are a commitment to change in the scientific community, which could be facilitated by a broad discussion of the vision, and obtaining necessary resources to enhance current knowledge of pathway perturbations and pathway assays in humans and to implement computational systems biology models. Implementation of these strategies would result in a new toxicity testing paradigm firmly based on human biology.

1,398 citations


Journal ArticleDOI
18 Mar 2010-Nature
TL;DR: Comparison of genomes of three phenotypically diverse Fusarium species revealed lineage-specific genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome, putting the evolution of fungal pathogenicity into a new perspective.
Abstract: Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.

1,386 citations


Journal ArticleDOI
TL;DR: A meta-analysis suggests that nitrogen deposition impedes organic matter decomposition, and thus stimulates carbon sequestration, in temperate forest soils where nitrogen is not limiting microbial growth as mentioned in this paper, and the concomitant reduction in soil carbon emissions is substantial, and equivalent in magnitude to the amount of carbon taken up by trees owing to nitrogen fertilization.
Abstract: The use of fossil fuels and fertilizers has increased the amount of biologically reactive nitrogen in the atmosphere over the past century. As a consequence, forests in industrialized regions have experienced greater rates of nitrogen deposition in recent decades. This unintended fertilization has stimulated forest growth, but has also affected soil microbial activity, and thus the recycling of soil carbon and nutrients. A meta-analysis suggests that nitrogen deposition impedes organic matter decomposition, and thus stimulates carbon sequestration, in temperate forest soils where nitrogen is not limiting microbial growth. The concomitant reduction in soil carbon emissions is substantial, and equivalent in magnitude to the amount of carbon taken up by trees owing to nitrogen fertilization. As atmospheric nitrogen levels continue to rise, increased nitrogen deposition could spread to older, more weathered soils, as found in the tropics; however, soil carbon cycling in tropical forests cannot yet be assessed.

1,275 citations


Journal ArticleDOI
TL;DR: LandTrendr (Landsat-based detection of Trends in Disturbance and Recovery), a new approach to extract spectral trajectories of land surface change from yearly Landsat time-series stacks, appears to be a feasible and robust means of increasing information extraction from the Landsat archive.

Journal ArticleDOI
TL;DR: This work identifies and discusses those problems for which genomics will be most valuable for curbing the accelerating worldwide loss of biodiversity and provides guidance on whichgenomics tools and approaches will bemost appropriate to use for different aspects of conservation.
Abstract: We will soon have complete genome sequences from thousands of species, as well as from many individuals within species. This coming explosion of information will transform our understanding of the amount, distribution and functional significance of genetic variation in natural populations. Now is a crucial time to explore the potential implications of this information revolution for conservation genetics and to recognize limitations in applying genomic tools to conservation issues. We identify and discuss those problems for which genomics will be most valuable for curbing the accelerating worldwide loss of biodiversity. We also provide guidance on which genomics tools and approaches will be most appropriate to use for different aspects of conservation.

Journal ArticleDOI
TL;DR: Comparisons of DNA methylation in eight diverse plant and animal genomes found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals.
Abstract: Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. Although DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylation throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honey bee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes.

Journal ArticleDOI
TL;DR: The results suggest that like in animals, NMD and RUST may be widespread in plants and may play important roles in regulating gene expression.
Abstract: Alternative splicing can enhance transcriptome plasticity and proteome diversity. In plants, alternative splicing can be manifested at different developmental stages, and is frequently associated with specific tissue types or environmental conditions such as abiotic stress. We mapped the Arabidopsis transcriptome at single-base resolution using the Illumina platform for ultrahigh-throughput RNA sequencing (RNA-seq). Deep transcriptome sequencing confirmed a majority of annotated introns and identified thousands of novel alternatively spliced mRNA isoforms. Our analysis suggests that at least approximately 42% of intron-containing genes in Arabidopsis are alternatively spliced; this is significantly higher than previous estimates based on cDNA/expressed sequence tag sequencing. Random validation confirmed that novel splice isoforms empirically predicted by RNA-seq can be detected in vivo. Novel introns detected by RNA-seq were substantially enriched in nonconsensus terminal dinucleotide splice signals. Alternative isoforms with premature termination codons (PTCs) comprised the majority of alternatively spliced transcripts. Using an example of an essential circadian clock gene, we show that intron retention can generate relatively abundant PTC(+) isoforms and that this specific event is highly conserved among diverse plant species. Alternatively spliced PTC(+) isoforms can be potentially targeted for degradation by the nonsense mediated mRNA decay (NMD) surveillance machinery or regulate the level of functional transcripts by the mechanism of regulated unproductive splicing and translation (RUST). We demonstrate that the relative ratios of the PTC(+) and reference isoforms for several key regulatory genes can be considerably shifted under abiotic stress treatments. Taken together, our results suggest that like in animals, NMD and RUST may be widespread in plants and may play important roles in regulating gene expression.

Journal ArticleDOI
TL;DR: The isolation of Candidatus “Nitrosopumilus maritimus” strain SCM1 is reported, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria.
Abstract: Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. The isolation of Candidatus “Nitrosopumilus maritimus” strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. Here we report the 1,645,259-bp closed genome of strain SCM1, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria. Consistent with in situ isotopic studies of marine archaea, the genome sequence indicates N. maritimus grows autotrophically using a variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon assimilation, while maintaining limited capacity for assimilation of organic carbon. This unique instance of archaeal biosynthesis of the osmoprotectant ectoine and an unprecedented enrichment of multicopper oxidases, thioredoxin-like proteins, and transcriptional regulators points to an organism responsive to environmental cues and adapted to handling reactive copper and nitrogen species that likely derive from its distinctive biochemistry. The conservation of N. maritimus gene content and organization within marine metagenomes indicates that the unique physiology of these specialized oligophiles may play a significant role in the biogeochemical cycles of carbon and nitrogen.

Journal ArticleDOI
TL;DR: In this article, the authors summarize more than 180 site years of eddy covariance measurements of carbon dioxide flux made at forest chronosequences in North America and show that carbon loss from all ecosystems following a stand-replacing disturbance, becoming a carbon sink by 20 years for all ecosystems and by 10 years for most.
Abstract: Disturbances are important for renewal of North American forests. Here we summarize more than 180 site years of eddy covariance measurements of carbon dioxide flux made at forest chronosequences in North America. The disturbances included stand-replacing fire (Alaska, Arizona, Manitoba, and Saskatchewan) and harvest (British Columbia, Florida, New Brunswick, Oregon, Quebec, Saskatchewan, and Wisconsin) events, insect infestations (gypsy moth, forest tent caterpillar, and mountain pine beetle), Hurricane Wilma, and silvicultural thinning (Arizona, California, and New Brunswick). Net ecosystem production (NEP) showed a carbon loss from all ecosystems following a stand-replacing disturbance, becoming a carbon sink by 20 years for all ecosystems and by 10 years for most. Maximum carbon losses following disturbance (g C m−2y−1) ranged from 1270 in Florida to 200 in boreal ecosystems. Similarly, for forests less than 100 years old, maximum uptake (g C m−2y−1) was 1180 in Florida mangroves and 210 in boreal ecosystems. More temperate forests had intermediate fluxes. Boreal ecosystems were relatively time invariant after 20 years, whereas western ecosystems tended to increase in carbon gain over time. This was driven mostly by gross photosynthetic production (GPP) because total ecosystem respiration (ER) and heterotrophic respiration were relatively invariant with age. GPP/ER was as low as 0.2 immediately following stand-replacing disturbance reaching a constant value of 1.2 after 20 years. NEP following insect defoliations and silvicultural thinning showed lesser changes than stand-replacing events, with decreases in the year of disturbance followed by rapid recovery. NEP decreased in a mangrove ecosystem following Hurricane Wilma because of a decrease in GPP and an increase in ER.

Journal ArticleDOI
TL;DR: It is suggested that the classical model of adaptive radiation, where morphological evolution is initially rapid and slows through time, may be rare in comparative data.
Abstract: George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations-more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed by relative stasis. We compared the fit of this model to both single selective peak and random walk models. We found little support for the early-burst model of adaptive radiation, whereas both other models, particularly that of selective peaks, were commonly supported. In addition, we found that the net rate of morphological evolution varied inversely with clade age. The youngest clades appear to evolve most rapidly because long-term change typically does not attain the amount of divergence predicted from rates measured over short time scales. Across our entire analysis, the dominant pattern was one of constraints shaping evolution continually through time rather than rapid evolution followed by stasis. We suggest that the classical model of adaptive radiation, where morphological evolution is initially rapid and slows through time, may be rare in comparative data.

Journal ArticleDOI
TL;DR: It is shown that IgT, an immunoglobulin isotype of unknown function, acts like a mucosal antibody, and detected responses of rainbow trout IgT to an intestinal parasite only in the gut, whereas IgM responses were confined to the serum.
Abstract: Teleost fish are the most primitive bony vertebrates that contain immunoglobulins. In contrast to mammals and birds, these species are devoid of immunoglobulin A (IgA) or a functional equivalent. This observation suggests that specialization of immunoglobulin isotypes into mucosal and systemic responses took place during tetrapod evolution. Challenging that paradigm, here we show that IgT, an immunoglobulin isotype of unknown function, acts like a mucosal antibody. We detected responses of rainbow trout IgT to an intestinal parasite only in the gut, whereas IgM responses were confined to the serum. IgT coated most intestinal bacteria. As IgT and IgA are phylogenetically distant immunoglobulins, their specialization into mucosal responses probably occurred independently by a process of convergent evolution.

Journal ArticleDOI
TL;DR: The roots of this perspective are traced, three overarching constructionist findings are presented, and fruitful directions for policy-relevant research in a social constructionist tradition are discussed.
Abstract: The social construction of illness is a major research perspective in medical sociology. This article traces the roots of this perspective and presents three overarching constructionist findings. First, some illnesses are particularly embedded with cultural meaning—which is not directly derived from the nature of the condition—that shapes how society responds to those afflicted and influences the experience of that illness. Second, all illnesses are socially constructed at the experiential level, based on how individuals come to understand and live with their illness. Third, medical knowledge about illness and disease is not necessarily given by nature but is constructed and developed by claims-makers and interested parties. We address central policy implications of each of these findings and discuss fruitful directions for policy-relevant research in a social constructionist tradition. Social constructionism provides an important counterpoint to medicine’s largely deterministic approaches to disease and ...

Journal ArticleDOI
TL;DR: In this article, the Delphi technique has been used to identify and qualify potential expert panelists according to objective guidelines and select appropriate parameters of the study such as the number of panelists, number of rounds, type of feedback, and measure of consensus.
Abstract: Construction engineering and management CEM researchers often rely on alternative research techniques when traditional methods fail. For example, surveys, interviews, and group-brainstorming techniques may not be appropriate for research that involves confounding factors and requires access to sensitive data. In such an environment, the Delphi technique allows researchers to obtain highly reliable data from certified experts through the use of strategically designed surveys. At present, the Delphi method has not seen widespread use in CEM research. This is likely due to variation among studies that implement Delphi in CEM research and ambiguity in literature that provides guidance for the specific parameters associated with the method. Using the guidance in this paper, the reader may: 1 understand the merits, appropriate application, and appropriate procedure of the traditional Delphi process; 2 identify and qualify potential expert panelists according to objective guidelines; 3 select the appropriate parameters of the study such as the number of panelists, number of rounds, type of feedback, and measure of consensus; 4 identify potential biases that may negatively impact the quality of the results; and 5 appropriately structure the surveys and conduct the process in such a way that bias is minimized or eliminated.

Journal ArticleDOI
TL;DR: In this article, a study of water isotopes in an Oregon watershed suggests that trees and streams tap into separate water reservoirs instead of using translatory flow, which assumes that water at any soil depth is well mixed.
Abstract: Water movement in upland humid watersheds from the soil surface to the stream is often described using the concept of translatory flow, which assumes that water at any soil depth is well mixed. A study of water isotopes in an Oregon watershed instead suggests that trees and streams tap into separate water reservoirs.

Journal ArticleDOI
TL;DR: A recent dive with the JAMSTEC Shinkai 6500 manned submersible in the Mariana fore arc southeast of Guam has discovered that MORB-like tholeiitic basalts crop out over large areas.
Abstract: Recent diving with the JAMSTEC Shinkai 6500 manned submersible in the Mariana fore arc southeast of Guam has discovered that MORB-like tholeiitic basalts crop out over large areas These ''fore-arc basalts'' (FAB) underlie boninites and overlie diabasic and gabbroic rocks Potential origins include eruption at a spreading center before subduction began or eruption during near-trench spreading after subduction began FAB trace element patterns are similar to those of MORB and most Izu-Bonin-Mariana (IBM) back-arc lavas However, Ti/V and Yb/V ratios are lower in FAB reflecting a stronger prior depletion of their mantle source compared to the source of basalts from mid-ocean ridges and back-arc basins Some FAB also have higher concentrations of fluid-soluble elements than do spreading center lavas Thus, the most likely origin of FAB is that they were the first lavas to erupt when the Pacific Plate began sinking beneath the Philippine Plate at about 51 Ma The magmas were generated by mantle decompression during near-trench spreading with little or no mass transfer from the subducting plate Boninites were generated later when the residual, highly depleted mantle melted at shallow levels after fluxing by a water-rich fluid derived from the sinking Pacific Plate This magmatic stratigraphy of FAB overlain by transitional lavas and boninites is similar to that found in many ophiolites, suggesting that ophiolitic assemblages might commonly originate from near-trench volcanism caused by subduction initiation Indeed, the widely dispersed Jurassic and Cretaceous Tethyan ophiolites could represent two such significant subduction initiation events

Journal ArticleDOI
TL;DR: It is demonstrated that variations of absolute humidity explain both the onset of wintertime influenza transmission and the overarching seasonality of this pathogen in temperate regions.
Abstract: Much of the observed wintertime increase of mortality in temperate regions is attributed to seasonal influenza. A recent reanalysis of laboratory experiments indicates that absolute humidity strongly modulates the airborne survival and transmission of the influenza virus. Here, we extend these findings to the human population level, showing that the onset of increased wintertime influenza-related mortality in the United States is associated with anomalously low absolute humidity levels during the prior weeks. We then use an epidemiological model, in which observed absolute humidity conditions temper influenza transmission rates, to successfully simulate the seasonal cycle of observed influenza-related mortality. The model results indicate that direct modulation of influenza transmissibility by absolute humidity alone is sufficient to produce this observed seasonality. These findings provide epidemiological support for the hypothesis that absolute humidity drives seasonal variations of influenza transmission in temperate regions.

Journal ArticleDOI
TL;DR: Given the multipart nature of the seed, the requirements imposed upon it in addition to completing germination (which involves only a limited number of cells), the challenge to identify ‘germination-completion’ genes is large and there are limited opportunities at present for improving germination through genetic manipulation.

Journal ArticleDOI
01 Apr 2010-Ecology
TL;DR: A "Dilution Recoupling Hypothesis" is described that focuses on the balance between phytoplankton growth and grazing, and the seasonally varying physical processes influencing this balance.
Abstract: The Critical Depth Hypothesis formalized by Sverdrup in 1953 posits that vernal phytoplankton blooms occur when surface mixing shoals to a depth shallower than a critical depth horizon defining the point where phytoplankton growth exceeds losses. This hypothesis has since served as a cornerstone in plankton ecology and reflects the very common assumption that blooms are caused by enhanced growth rates in response to improved light, temperature, and stratification conditions, not simply correlated with them. Here, a nine-year satellite record of phytoplankton biomass in the subarctic Atlantic is used to reevaluate seasonal plankton dynamics. Results show that (1) bloom initiation occurs in the winter when mixed layer depths are maximum, not in the spring, (2) coupling between phytoplankton growth (l) and losses increases during spring stratification, rather than decreases, (3) maxima in net population growth rates (r) are as likely to occur in midwinter as in spring, and (4) r is generally inversely related to l. These results are incompatible with the Critical Depth Hypothesis as a functional framework for understanding bloom dynamics. In its place, a ''Dilution-Recoupling Hypothesis'' is described that focuses on the balance between phytoplankton growth and grazing, and the seasonally varying physical processes influencing this balance. This revised view derives from fundamental concepts applied during field dilution experiments, builds upon earlier modeling results, and is compatible with observed phytoplankton blooms in the absence of spring mixed layer shoaling.

Journal ArticleDOI
TL;DR: In this paper, a well-to-pump life cycle assessment (LCA) was performed to investigate the overall sustainability and net energy balance of an algal biodiesel process.
Abstract: Algae biomass has great promise as a sustainable alternative to conventional transportation fuels. In this study, a well-to-pump life cycle assessment (LCA) was performed to investigate the overall sustainability and net energy balance of an algal biodiesel process. The goal of this LCA was to provide baseline information for the algae biodiesel process. The functional unit was 1,000 MJ of energy from algal biodiesel using existing technology. Systematic boundary identification was performed using relative mass, energy, and economic value method using a 5% cutoff value. Primary data for this study were obtained from The USLCI database and the Greenhouse Gases, Regulated Emissions and Energy use in Transportation model. Carbohydrates in coproducts from algae biodiesel production were assumed to displace corn as a feedstock for ethanol production. For every 24 kg of algal biodiesel produced (1,000 MJ algae biodiesel), 34 kg coproducts are also produced. Total energy input without solar drying is 3,292 and 6,194 MJ for the process with filter press and centrifuge as the initial filtering step, respectively. Net CO2 emissions are −20.9 and 135.7 kg/functional unit for a process utilizing a filter press and centrifuge, respectively. In addition to the −13.96 kg of total air emissions per functional unit, 18.6 kg of waterborne wastes, 0.28 kg of solid waste, and 5.54 Bq are emitted. The largest energy input (89%) is in the natural gas drying of the algal cake. Although net energy for both filter press and centrifuge processes are −6,670 and −3,778 MJ/functional unit, respectively, CO2 emissions are positive for the centrifuge process while they are negative for the filter press process. Additionally, 20.4 m3 of wastewater per functional unit is lost from the growth ponds during the 4-day growth cycle due to evaporation. This LCA has quantified one major obstacle in algae technology: the need to efficiently process the algae into its usable components. Thermal dewatering of algae requires high amounts of fossil fuel derived energy (3,556 kJ/kg of water removed) and consequently presents an opportunity for significant reduction in energy use. The potential of green algae as a fuel source is not a new idea; however, this LCA and other sources clearly show a need for new technologies to make algae biofuels a sustainable, commercial reality.

Journal ArticleDOI
TL;DR: The strong influence of economic and demographic variables on the levels of invasion by alien species demonstrates that future solutions to the problem of biological invasions at a national scale lie in mitigating the negative environmental consequences of human activities that generate wealth and by promoting more sustainable population growth.
Abstract: The accelerating rates of international trade, travel, and transport in the latter half of the twentieth century have led to the progressive mixing of biota from across the world and the number of species introduced to new regions continues to increase. The importance of biogeographic, climatic, economic, and demographic factors as drivers of this trend is increasingly being realized but as yet there is no consensus regarding their relative importance. Whereas little may be done to mitigate the effects of geography and climate on invasions, a wider range of options may exist to moderate the impacts of economic and demographic drivers. Here we use the most recent data available from Europe to partition between macroecological, economic, and demographic variables the variation in alien species richness of bryophytes, fungi, vascular plants, terrestrial insects, aquatic invertebrates, fish, amphibians, reptiles, birds, and mammals. Only national wealth and human population density were statistically significant predictors in the majority of models when analyzed jointly with climate, geography, and land cover. The economic and demographic variables reflect the intensity of human activities and integrate the effect of factors that directly determine the outcome of invasion such as propagule pressure, pathways of introduction, eutrophication, and the intensity of anthropogenic disturbance. The strong influence of economic and demographic variables on the levels of invasion by alien species demonstrates that future solutions to the problem of biological invasions at a national scale lie in mitigating the negative environmental consequences of human activities that generate wealth and by promoting more sustainable population growth.

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TL;DR: Overall, parental social support demonstrated positive effects and the majority of studies demonstrated positive associations among selected measures of parental tangible and intangible social support and youth activity.
Abstract: Social support from parents serves as one of the primary influences of youth physical activity-related behaviors. A systematic review was conducted on the relationship of parental social support to the physical activity-related behaviors of youth. Four categories of social support were identified, falling under two distinct mechanisms-tangible and intangible. Tangible social support is divided into two categories: instrumental-purchasing equipment/payment of fees and transportation-and conditional-doing activity with and watching/supervision. Intangible social support is divided into the two categories of motivational- encouragement and praise-and informational-discussing benefits of. The majority of studies demonstrated positive associations among selected measures of parental tangible and intangible social support and youth activity. Overall, parental social support demonstrated positive effects. Many studies, however, combine social support categories and/or respondents into composite measures, making it difficult to disentangle the specific effects of parents and the type of support provided.

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TL;DR: Sequence diagrams document the interoperability of the analysis classes for solving nonlinear finite-element equations, demonstrating that object composition with design patterns provides a general approach to developing and refactoring nonlinear infinite-element software.
Abstract: Object composition offers significant advantages over class inheritance to develop a flexible software architecture for finite-element analysis. Using this approach, separate classes encapsulate fu...