Showing papers by "University of Georgia published in 2013"

The global distribution and burden of dengue

Abstract: Dengue is a systemic viral infection transmitted between humans by Aedes mosquitoes. For some patients, dengue is a life-threatening illness. There are currently no licensed vaccines or specific therapeutics, and substantial vector control efforts have not stopped its rapid emergence and global spread. The contemporary worldwide distribution of the risk of dengue virus infection and its public health burden are poorly known. Here we undertake an exhaustive assembly of known records of dengue occurrence worldwide, and use a formal modelling framework to map the global distribution of dengue risk. We then pair the resulting risk map with detailed longitudinal information from dengue cohort studies and population surfaces to infer the public health burden of dengue in 2010. We predict dengue to be ubiquitous throughout the tropics, with local spatial variations in risk influenced strongly by rainfall, temperature and the degree of urbanization. Using cartographic approaches, we estimate there to be 390 million (95% credible interval 284-528) dengue infections per year, of which 96 million (67-136) manifest apparently (any level of disease severity). This infection total is more than three times the dengue burden estimate of the World Health Organization. Stratification of our estimates by country allows comparison with national dengue reporting, after taking into account the probability of an apparent infection being formally reported. The most notable differences are discussed. These new risk maps and infection estimates provide novel insights into the global, regional and national public health burden imposed by dengue. We anticipate that they will provide a starting point for a wider discussion about the global impact of this disease and will help to guide improvements in disease control strategies using vaccine, drug and vector control methods, and in their economic evaluation.

Photoremovable Protecting Groups in Chemistry and Biology: Reaction Mechanisms and Efficacy

Abstract: The review covers the knowledge on photoremovable protecting groups and includes all relevant chromophores studied in the time period of 2000–2012; the most relevant earlier works are also discussed.

Noncanonical Inflammasome Activation by Intracellular LPS Independent of TLR4

Abstract: Gram-negative bacteria including Escherichia coli, Citrobacter rodentium, Salmonella typhimurium, and Shigella flexneri are sensed in an ill-defined manner by an intracellular inflammasome complex that activates caspase-11. We show that macrophages loaded with synthetic lipid A, E. coli lipopolysaccharide (LPS), or S. typhimurium LPS activate caspase-11 independently of the LPS receptor Toll-like receptor 4 (TLR4). Consistent with lipid A triggering the noncanonical inflammasome, LPS containing a divergent lipid A structure antagonized caspase-11 activation in response to E. coli LPS or Gram-negative bacteria. Moreover, LPS-mutant E. coli failed to activate caspase-11. Tlr4(-/-) mice primed with TLR3 agonist polyinosinic:polycytidylic acid [poly(I:C)] to induce pro-caspase-11 expression were as susceptible as wild-type mice were to sepsis induced by E. coli LPS. These data unveil a TLR4-independent mechanism for innate immune recognition of LPS.

The changing carbon cycle of the coastal ocean

Abstract: The carbon cycle of the coastal ocean is a dynamic component of the global carbon budget. But the diverse sources and sinks of carbon and their complex interactions in these waters remain poorly understood. Here we discuss the sources, exchanges and fates of carbon in the coastal ocean and how anthropogenic activities have altered the carbon cycle. Recent evidence suggests that the coastal ocean may have become a net sink for atmospheric carbon dioxide during post-industrial times. Continued human pressures in coastal zones will probably have an important impact on the future evolution of the coastal ocean's carbon budget.

Draft genome sequence of chickpea ( Cicer arietinum ) provides a resource for trait improvement

Abstract: Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ~738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea—desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.

Justice at the millennium, a decade later: a meta-analytic test of social exchange and affect-based perspectives.

Abstract: Although a flurry of meta-analyses summarized the justice literature at the turn of the millennium, interest in the topic has surged in the decade since. In particular, the past decade has witnessed the rise of social exchange theory as the dominant lens for examining reactions to justice, and the emergence of affect as a complementary lens for understanding such reactions. The purpose of this meta-analytic review was to test direct, mediating, and moderating hypotheses that were inspired by those 2 perspectives, to gauge their adequacy as theoretical guides for justice research. Drawing on a review of 493 independent samples, our findings revealed a number of insights that were not included in prior meta-analyses. With respect to social exchange theory, our results revealed that the significant relationships between justice and both task performance and citizenship behavior were mediated by indicators of social exchange quality (trust, organizational commitment, perceived organizational support, and leader‐member exchange), though such mediation was not apparent for counterproductive behavior. The strength of those relationships did not vary according to whether the focus of the justice matched the target of the performance behavior, contrary to popular assumptions in the literature, or according to whether justice was referenced to a specific event or a more general entity. With respect to affect, our results showed that justice‐performance relationships were mediated by positive and negative affect, with the relevant affect dimension varying across justice and performance variables. Our discussion of these findings focuses on the merit in integrating the social exchange and affect lenses in future research.

Climate Change and Infectious Diseases: From Evidence to a Predictive Framework

Abstract: Scientists have long predicted large-scale responses of infectious diseases to climate change, giving rise to a polarizing debate, especially concerning human pathogens for which socioeconomic drivers and control measures can limit the detection of climate-mediated changes. Climate change has already increased the occurrence of diseases in some natural and agricultural systems, but in many cases, outcomes depend on the form of climate change and details of the host-pathogen system. In this review, we highlight research progress and gaps that have emerged during the past decade and develop a predictive framework that integrates knowledge from ecophysiology and community ecology with modeling approaches. Future work must continue to anticipate and monitor pathogen biodiversity and disease trends in natural ecosystems and identify opportunities to mitigate the impacts of climate-driven disease emergence.

The Dark Side of Analyst Coverage: The Case of Innovation

Abstract: We examine the effects of financial analysts on the real economy in the case of innovation. Our baseline results show that firms covered by a larger number of analysts generate fewer patents and patents with lower impact. To establish causality, we use a difference-in-differences approach that relies on the variation generated by multiple exogenous shocks to analyst coverage, as well as an instrumental variable approach. Our identification strategies suggest a negative causal effect of analyst coverage on firm innovation. The evidence is consistent with the hypothesis that analysts exert too much pressure on managers to meet short-term goals, impeding firms’ investment in long-term innovative projects. We further discuss possible underlying mechanisms through which analysts impede innovation and show that there is a residual effect of analysts on innovation even after controlling for these mechanisms. Our paper offers novel evidence on a previously under-explored adverse consequence of analyst coverage — its hindrance to firm innovation.

The genome of the pear (Pyrus bretschneideri Rehd.)

Abstract: Pear, the third most important temperate fruit species after grape and apple, belongs to the subfamily Pomoideae in the family Rosaceae. The majority of cultivated pears are functional diploids (2n = 34). As a popular fruit in the world market, pear has widespread cultivation on six continents, with major production in China, the United States, Italy, Argentina, and Spain (Supplemental Fig. 1). Pears are among the oldest of the world's fruit crops, with >3000 yr of cultivation history (Lombard and Westwood 1987), likely originating during the Tertiary period (65–55 million years ago [MYA]) in the mountainous regions of southwestern China and, from there, spreading on to both the East and West (Rubtsov 1944; Zeven and Zhukovsky 1975). Central Asia and eastern China are identified as two subcenters of genetic diversity for pear (Vavilov 1951). The Pyrus genus is genetically diverse with thousands of cultivars, but it can be divided into two major groups, Occidental pears (European pears) and Oriental pears (Asiatic pears). At least 22 primary species are well-recognized in Pyrus; however, only a few species, including Pyrus bretschneideri, Pyrus pyrifolia, Pyrus ussuriensis, Pyrus sinkiangensis, and Pyrus communis, have been utilized for fruit production. Herein, we report on a high-quality draft genome sequence of the diploid P. bretschneideri Rehd. cv. ‘Dangshansuli’ (also known as ‘Suli’), the most important commercial Asiatic pear cultivar grown in the world (>4 million tons per year), having >500 yr of cultivated history in China. Pear is highly heterozygous due to self-incompatibility and interspecies compatibility. The genome is known to have an abundance of repetitive DNA sequences. In this study, a novel combination of BAC-by-BAC (bacterial artificial chromosome) strategy, with Illumina sequencing technology, is used for the first time for de novo assembly of a highly heterozygous genome of this size with highly repetitive DNA sequences. This has demonstrated that a complex plant genome sequence can be assembled and characterized using these technologies without the availability of a physical reference. Additionally, we also report on primary factors contributing to genome size differences between pear and apple, both belonging to the subfamily Pomoideae; chromosomal evolution of Rosaceae; and genes controlling valuable traits of pear, including self-incompatibility, lignified stone cells in flesh of fruit (unique to pear), sugar, and aroma.

Identification of seven loci affecting mean telomere length and their association with disease

Abstract: Interindividual variation in mean leukocyte telomere length (LTL) is associated with cancer and several age-associated diseases. We report here a genome-wide meta-analysis of 37,684 individuals with replication of selected variants in an additional 10,739 individuals. We identified seven loci, including five new loci, associated with mean LTL (P < 5 × 10(-8)). Five of the loci contain candidate genes (TERC, TERT, NAF1, OBFC1 and RTEL1) that are known to be involved in telomere biology. Lead SNPs at two loci (TERC and TERT) associate with several cancers and other diseases, including idiopathic pulmonary fibrosis. Moreover, a genetic risk score analysis combining lead variants at all 7 loci in 22,233 coronary artery disease cases and 64,762 controls showed an association of the alleles associated with shorter LTL with increased risk of coronary artery disease (21% (95% confidence interval, 5-35%) per standard deviation in LTL, P = 0.014). Our findings support a causal role of telomere-length variation in some age-related diseases.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Abstract: Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.

Post-qualitative research

Abstract: There are three aspects of this special issue that we as co-editors want to draw to your attention. The first is that we are, finally, “after” the decade of SRE able to ask what comes next for qual...

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Abstract: Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. (Continued on next page)

The 2013 release of cloudy

Abstract: This is a summary of the 2013 release of the plasma simulation code Cloudy. Cloudy models the ionization, chemical, and thermal state of material that may be exposed to an external radiation field or other source of heating, and predicts observables such as emission and absorption spectra. It works in terms of elementary processes, so is not limited to any particular temperature or density regime. This paper summarizes advances made since the last major review in 1998. Much of the recent development has emphasized dusty molecular environments, improvements to the ionization/chemistry solvers, and how atomic and molecular data are used. We present two types of simulations to demonstrate the capability of the code. We consider a molecular cloud irradiated by an X-ray source such as an active nucleus and show how treating EUV recombination lines and the full SED affects the observed spectrum. A second example illustrates the very wide range of particle and radiation density that can be considered.

Global Education Inc: new policy networks and the neo-liberal imaginary

Abstract: , by Stephen J Ball, Abingdon, Routledge, 2012, 163 pp, £2599 (paperback), ISBN 978-0-41-568410-1 We are having to be alert All of us around the globe The world is changing fast Its essential

Three decades of populist radical right parties in Western Europe: So what?

Abstract: The populist radical right constitutes the most successful party family in postwar Western Europe. Many accounts in both academia and the media warn of the growing influence of populist radical right parties (PRRPs), the so-called ‘verrechtsing’ (or right turn) of European politics, but few provide empirical evidence of it. This lecture provides a first comprehensive analysis of the alleged effects of the populist radical right on the people, parties, policies and polities of Western Europe. The conclusions are sobering. The effects are largely limited to the broader immigration issue, and even here PRRPs should be seen as catalysts rather than initiators, who are neither a necessary nor a sufficient condition for the introduction of stricter immigration policies. The lecture ends by providing various explanations for the limited impact of PRRPs, but it is also argued that populist parties are not destined for success in opposition and failure in government. In fact, there are at least three reasons why PRRPs might increase their impact in the near future: the tabloidisation of political discourse; the aftermath of the economic crisis; and the learning curve of PRRPs. Even in the unlikely event that PRRPs will become major players in West European politics, it is unlikely that this will lead to a fundamental transformation of the political system. PRRPs are not a normal pathology of European democracy, unrelated to its basic values, but a pathological normalcy, which strives for the radicalisation of mainstream values.

Agriculture: Feeding the future

Abstract: Humanity depends on fewer than a dozen of the approximately 300,000 species of flowering plants for 80% of its caloric intake. And we capitalize on only a fraction of the genetic diversity that resides within each of these species. This is not enough to support our food system in the future. Food availability must double in the next 25 years to keep pace with population and income growth around the world. Already, food-production systems are precarious in the face of intensifying demand, climate change, soil degradation and water and land shortages. Farmers have saved the seeds of hundreds of crop species and hundreds of thousands of ‘primitive’ varieties (local domesticates called landraces), as well as the wild relatives of crop species and modern varieties no longer in use. These are stored in more than 1,700 gene banks worldwide. Maintaining the 11 international gene-bank collections alone costs about US$18 million a year.

Birds of a Feather Tweet Together: Integrating Network and Content Analyses to Examine Cross-Ideology Exposure on Twitter

Abstract: This study integrates network and content analyses to examine exposure to cross-ideological political views on Twitter. We mapped the Twitter networks of 10 controversial political topics, discovered clusters - subgroups of highly self-connected users - and coded messages and links in them for political orientation. We found that Twitter users are unlikely to be exposed to cross-ideological content from the clusters of users they followed, as these were usually politically homogeneous. Links pointed at grassroots web pages e.g.: blogs more frequently than traditional media websites. Liberal messages, however, were more likely to link to traditional media. Last, we found that more specific topics of controversy had both conservative and liberal clusters, while in broader topics, dominant clusters reflected conservative sentiment.

Research collaboration in universities and academic entrepreneurship: the-state-of-the-art

Abstract: There is abundant evidence that research collaboration has become the norm in every field of scientific and technical research. We provide a critical overview of the literature on research collaboration, focusing particularly on individual-level collaborations among university researchers, but we also give attention to university researchers’ collaborations with researchers in other sectors, including industry. We consider collaborations aimed chiefly at expanding the base of knowledge (knowledge-focused collaborations) as well as ones focused on production of economic value and wealth (property-focused collaborations), the latter including most academic entrepreneurship research collaborations. To help organize our review we develop a framework for analysis, one that considers attributes of collaborators, collaborative process and organization characteristics as the affect collaboration choices and outcomes. In addition, we develop and use a “Propositional Table for Research Collaboration Literature,” presented as an “Appendix” to this study. We conclude with some suggestions for possible improvement in research on collaboration including: (1) more attention to multiple levels of analysis and the interactions among them; (2) more careful measurement of impacts as opposed to outputs; (3) more studies on ‘malpractice’ in collaboration, including exploitation; (4) increased attention to collaborators’ motives and the social psychology of collaborative teams.

Targeting global conservation funding to limit immediate biodiversity declines

Abstract: Inadequate funding levels are a major impediment to effective global biodiversity conservation and are likely associated with recent failures to meet United Nations biodiversity targets. Some countries are more severely underfunded than others and therefore represent urgent financial priorities. However, attempts to identify these highly underfunded countries have been hampered for decades by poor and incomplete data on actual spending, coupled with uncertainty and lack of consensus over the relative size of spending gaps. Here, we assemble a global database of annual conservation spending. We then develop a statistical model that explains 86% of variation in conservation expenditures, and use this to identify countries where funding is robustly below expected levels. The 40 most severely underfunded countries contain 32% of all threatened mammalian diversity and include neighbors in some of the world’s most biodiversity-rich areas (Sundaland, Wallacea, and Near Oceania). However, very modest increases in international assistance would achieve a large improvement in the relative adequacy of global conservation finance. Our results could therefore be quickly applied to limit immediate biodiversity losses at relatively little cost.

Evolving Views of Pectin Biosynthesis

Abstract: Recent progress in the identification and characterization of pectin biosynthetic proteins and the discovery of pectin domain–containing proteoglycans are changing our view of how pectin, the most complex family of plant cell wall polysaccharides, is synthesized. The functional confirmation of four types of pectin biosynthetic glycosyltransferases, the identification of multiple putative pectin glycosyl- and methyltransferases, and the characteristics of the GAUT1:GAUT7 homogalacturonan biosynthetic complex with its novel mechanism for retaining catalytic subunits in the Golgi apparatus and its 12 putative interacting proteins are beginning to provide a framework for the pectin biosynthetic process. We propose two partially overlapping hypothetical and testable models for pectin synthesis: the consecutive glycosyltransferase model and the domain synthesis model.

An interdisciplinary meta-analysis of the potential antecedents, correlates, and consequences of protégé perceptions of mentoring.

Abstract: This meta-analysis summarized youth, academic, and workplace research on the potential antecedents (demographics, human capital, and relationship attributes), correlates (interaction frequency, relationship length, performance, motivation, and social capital), and consequences (attitudinal, behavioral, career-related, and health-related outcomes) of protege perceptions of instrumental support, psychosocial support, and relationship quality to the mentor or to the relationship. A total of 173 meta-analytic correlations were computed based on data from 173 samples and a combined N of 40,737. Among antecedents, positive protege perceptions were most strongly associated with greater similarity in attitudes, values, beliefs, and personality with their mentors (ρ ranged from .38 to .59). Among correlates, protege perceptions of greater instrumental support (ρ = .35) and relationship quality (ρ = .54) were most strongly associated with social capital while protege perceptions of greater psychosocial support were most strongly associated with interaction frequency (ρ = .25). Among consequences, protege perceptions of greater instrumental support (ρ = .36) and relationship quality (ρ = .38) were most strongly associated with situational satisfaction while protege perceptions of psychosocial support were most highly associated with sense of affiliation (ρ = .41). Comparisons between academic and workplace mentoring generally revealed differences in magnitude, rather than direction, of the obtained effects. The results should be interpreted in light of the methodological limitations (primarily cross-sectional designs and single-source data) and, in some instances, a small number of primary studies.

The 2013 Release of Cloudy

Abstract: This is a summary of the 2013 release of the plasma simulation code Cloudy. Cloudy models the ionization, chemical, and thermal state of material that may be exposed to an external radiation field or other source of heating, and predicts observables such as emission and absorption spectra. It works in terms of elementary processes, so is not limited to any particular temperature or density regime. This paper summarizes advances made since the last major review in 1998. Much of the recent development has emphasized dusty molecular environments, improvements to the ionization / chemistry solvers, and how atomic and molecular data are used. We present two types of simulations to demonstrate the capability of the code. We consider a molecular cloud irradiated by an X-ray source such as an Active Nucleus and show how treating EUV recombination lines and the full SED affects the observed spectrum. A second example illustrates the very wide range of particle and radiation density that can be considered.

An Arabidopsis Cell Wall Proteoglycan Consists of Pectin and Arabinoxylan Covalently Linked to an Arabinogalactan Protein

Abstract: Plant cell walls are comprised largely of the polysaccharides cellulose, hemicellulose, and pectin, along with ∼10% protein and up to 40% lignin. These wall polymers interact covalently and noncovalently to form the functional cell wall. Characterized cross-links in the wall include covalent linkages between wall glycoprotein extensins between rhamnogalacturonan II monomer domains and between polysaccharides and lignin phenolic residues. Here, we show that two isoforms of a purified Arabidopsis thaliana arabinogalactan protein (AGP) encoded by hydroxyproline-rich glycoprotein family protein gene At3g45230 are covalently attached to wall matrix hemicellulosic and pectic polysaccharides, with rhamnogalacturonan I (RG I)/homogalacturonan linked to the rhamnosyl residue in the arabinogalactan (AG) of the AGP and with arabinoxylan attached to either a rhamnosyl residue in the RG I domain or directly to an arabinosyl residue in the AG glycan domain. The existence of this wall structure, named ARABINOXYLAN PECTIN ARABINOGALACTAN PROTEIN1 (APAP1), is contrary to prevailing cell wall models that depict separate protein, pectin, and hemicellulose polysaccharide networks. The modified sugar composition and increased extractability of pectin and xylan immunoreactive epitopes in apap1 mutant aerial biomass support a role for the APAP1 proteoglycan in plant wall architecture and function.

Short selling and the price discovery process

Abstract: We show that stock prices are more accurate when short sellers are more active First, in a large panel of NYSE-listed stocks, intraday informational efficiency of prices improves with greater shorting flow Second, at monthly and annual horizons, more shorting flow accelerates the incorporation of public information into prices Third, greater shorting flow reduces post-earnings-announcement drift for negative earnings surprises Fourth, short sellers change their trading around extreme return events in a way that aids price discovery and reduces divergence from fundamental values These results are robust to various econometric specifications, and their magnitude is economically meaningful The Author 2012 Published by Oxford University Press on behalf of The Society for Financial Studies All rights reserved For Permissions, please e-mail: journalspermissions@oupcom, Oxford University Press

Standard methods for varroa research

Abstract: SummaryVery rapidly after Varroa destructor invaded apiaries of Apis mellifera, the devastating effect of this mite prompted an active research effort to understand and control this parasite. Over a few decades, varroa has spread to most countries exploiting A. mellifera. As a consequence, a large number of teams have worked with this organism, developing a diversity of research methods. Often different approaches have been followed to achieve the same goal. The diversity of methods made the results difficult to compare, thus hindering our understanding of this parasite. In this paper, we provide easy to use protocols for the collection, identification, diagnosis, rearing, breeding, marking and measurement of infestation rates and fertility of V. destructor. We also describe experimental protocols to study orientation and feeding of the mite, to infest colonies or cells and measure the mite's susceptibility to acaricides. Where relevant, we describe which mite should be used for bioassays since their beha...