bluuebunny/crossref_metadata_2025_split huggingface dataset:
Invasion of exotic arthropods in South America's biodiversity hotspots and agro-production systems.
Authors: Wyckhuys K. A. G. , Kondo T. , Herrera B. V. , Miller D. R. , Naranjo N. , Hyman G. 
Published: July 2013

Abstract

This chapter presents a study attempting to document the most significant arthropod invasions in mainland South America, with particular emphasis on scales (e.g., Coccidae, Diaspididae and Pseudococcidae). A regional species inventory was developed, based upon (gray) literature revision, and employed niche modelling to visualize the geographical distribution of (potentially) some of the most worrisome species. A broad literature revision was carried out to screen invasive species records in mainland South America. Global (e.g., ISI Web of Knowledge, CAB Abstracts) and regional scientific literature databases (e.g., Scielo) were consulted and queries were formulated for invasive or exotic arthropods. For invasive scales, expert knowledge, e.g., TK, DRM or ALP and specialized databases such as ScaleNet were consulted. Focusing monitoring activities on potential ports of entry could be an effective and relatively low-cost option for early detection of invasive species that enter through cargo or passenger transport.
Insect Life Cycle Modelling (ILCYM) software - a new tool for regional and global insect pest risk assessments under current and future climate change scenarios.
Authors: Sporleder M. , Tonnang H. E. Z. , Carhuapoma P. , Gonzales J. C. , Juarez H. , Kroschel J. 
Published: July 2013

Abstract

This chapter describes the application of ILCYM (Insect Life Cycle Modelling) software, which supports the development of process-oriented temperature-driven and age-stage structured insect phenology/population models. ILCYM interactively leads the user through the steps for developing insect phenology models, for conducting simulations, and for producing potential population distribution and risk mapping under current or future temperature (climate change) scenarios. The phenology model developed for the potato tuber moth Phthorimaea operculella (Lepidoptera: Gelechiidae) is used to demonstrate the resulting modelling outputs.
Tege Imperium!: A Defence of Empire
Authors: Foster Russell 
Published: July 2013

Abstract‘Empire’ is a pejorative word in contemporary political science, a term which no longer describes a system of government and social organisation but which now serves only as an unflattering term, an accusation levelled against undesirable polities and policies. In the collective minds of academia and the community, moreover, ‘empire’ is either a concept with many meanings and applications, or simply a catch-all word for the violence and oppression of previous political systems. This paper returns to the roots of the word itself in an effort to distil if not definite, then at least manageable, concepts: imperium and patrocinium. Identifying how patrocinium has begun to emerge in the twenty-first century, the paper argues that ultimately, this form of empire has much to offer, both conceptually and politically, in the modern world.
Different Realities: Academics, Politics, and International Relations
Authors: Romaniuk Scott Nicholas 
Published: July 2013

Abstract
Since the conception of International Relations (IR) as an academic discipline it has been characterized by prodigious interaction between academics and practitioners with the former often spending time in the policy arena before focusing on pedagogy. While a high level of interchange is held to be a defining characteristic of the American system, concern has been growing that there is an ever-widening gap between academics and practitioners and between theory and practice. Responding to the danger of a ‘me-cleaver-you-stupid’ form of theoretical and academic superiority, William Wallace conjectured his view of academic “semi-detachment”. In spite of a long history of government-academy co-operation, many social scientists are becoming increasing removed from the world of policy and action. This essay demonstrates that despite the subsequent criticisms levelled at Wallace, his general line of argumentation provides valuable insight into assuming a more useful and positive trajectory not only for scholars within the discipline but for the very field of IR itself.
Towards building a disease-phenotype knowledge base: extracting disease-manifestation relationship from literature
Authors: Xu Rong , Li Li , Wang QuanQiu 
Published: July 2013

Abstract
Motivation: Systems approaches to studying phenotypic relationships among diseases are emerging as an active area of research for both novel disease gene discovery and drug repurposing. Currently, systematic study of disease phenotypic relationships on a phenome-wide scale is limited because large-scale machine-understandable disease–phenotype relationship knowledge bases are often unavailable. Here, we present an automatic approach to extract disease–manifestation (D-M) pairs (one specific type of disease–phenotype relationship) from the wide body of published biomedical literature.
Data and Methods: Our method leverages external knowledge and limits the amount of human effort required. For the text corpus, we used 119 085 682 MEDLINE sentences (21 354 075 citations). First, we used D-M pairs from existing biomedical ontologies as prior knowledge to automatically discover D-M–specific syntactic patterns. We then extracted additional pairs from MEDLINE using the learned patterns. Finally, we analysed correlations between disease manifestations and disease-associated genes and drugs to demonstrate the potential of this newly created knowledge base in disease gene discovery and drug repurposing.
Results: In total, we extracted 121 359 unique D-M pairs with a high precision of 0.924. Among the extracted pairs, 120 419 (99.2%) have not been captured in existing structured knowledge sources. We have shown that disease manifestations correlate positively with both disease-associated genes and drug treatments.
Conclusions: The main contribution of our study is the creation of a large-scale and accurate D-M phenotype relationship knowledge base. This unique knowledge base, when combined with existing phenotypic, genetic and proteomic datasets, can have profound implications in our deeper understanding of disease etiology and in rapid drug repurposing.
Availability: http://nlp.case.edu/public/data/DMPatternUMLS/
Contact: rxx@case.edu
Scalable metagenomic taxonomy classification using a reference genome database
Authors: Ames Sasha K. , Hysom David A. , Gardner Shea N. , Lloyd G. Scott , Gokhale Maya B. , Allen Jonathan E. 
Published: July 2013

Abstract
Motivation: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge.
Results: A method is presented to shift computational costs to an off-line computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take &lt;20 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample.
Availability: Software was implemented in C++ and is freely available at http://sourceforge.net/projects/lmat
Contact: allen99@llnl.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Selection for a floral trait is not mediated by pollen receipt even though seed set in the population is pollen‐limited
Authors: Campbell Diane R. , Bischoff Mascha 
Published: July 2013

SummarySeed production in natural populations is often limited by quantity of pollen received. This pollen limitation has the potential to generate natural selection through female function favouring certain floral traits (hereafter ‘pollen‐mediated’ selection). Floral traits can, however, also be under selection via other mechanisms, and the influence of a particular trait on pollen limitation of individuals is rarely quantified.We took a trait‐based approach to pollen limitation by adding a quantitative trait to a previously published model. The modified model predicted impacts of both pollen supplementation and pollen reduction in seed production when the trait influences pollen receipt, and when the trait influences other model parameters. We then manipulated pollen availability in a population of the alpine New Zealand herbWahlenbergia albomarginatavarying in petal colour to test a long‐standing hypothesis that pale flower colour in that habitat is selected for via pollinators.Under pollen‐mediated selection, supplementing pollination should eliminate fitness dependence on a trait, while reducing pollination could exacerbate it. In contrast, if selection through female function on a floral trait is not solely pollen‐mediated, seed production should change with the trait value even when excess pollen is added. Furthermore, if the effect is on maximum seed production, the trait effect should increase with higher pollen availability as greater resources can be used for filling seeds from more fertilised ovules.InWahlenbergia albomarginata, average seed production was strongly pollen‐limited, with supplemental pollen increasing seeds by 43%. Selection through female function also favoured whiter flowers as quantified with reflectance spectrometry. This selection on flower colour was stronger when supplemental pollen was added, consistent with an effect of the trait on asymptotic seed production rather than an effect on pollen receipt.These results, along with previous behavioural studies of pollinators, show that pale flower colour, common in the habitat and often attributed to pollinator behaviour, is not maintained by pollen‐mediated selection but instead through another mechanism. This study illustrates the value of combining experimental pollen supplements and reductions with trait variation to study selection of floral traits, especially in species where compatible pollen receipt is difficult to measure.
Phloem‐feeding whiteflies can fool their host plants, but not their parasitoids
Authors: Zhang Peng‐Jun , Xu Cai‐Xia , Zhang Jin‐Ming , Lu Yao‐Bin , Wei Jia‐Ning , Liu Yin‐Quan , David Anja , Boland Wilhelm , Turlings Ted C. J. 
Published: July 2013

Summary

Herbivore attack induces plants to mobilize chemical defences, including the release of volatiles that attract natural enemies of the herbivore. This commonly involves the jasmonic acid (JA) pathway. However, phloem‐feeding whiteflies specifically trigger salicylic acid (SA)‐signalling, thereby suppressing JA‐based defences and enhancing host plant suitability.

Here, we show with Arabidopsis thaliana plants that the whitefly parasitoid Encarsia formosa outsmarts this apparent host plant manipulation by exploiting the SA‐triggered emission of β‐myrcene. Assays with various Arabidopsis mutants and phytohormone and gene‐expression analyses reveal that the whiteflies induce the accumulation of endogenous SA, thereby enhancing the expression of SA‐regulated genes, one of which encodes ocimene/myrcene synthase, which resulted in the recruitment of parasitoids under greenhouse conditions. Performance assays confirmed that whiteflies directly benefit from suppressing JA‐based defences.

Taken together, we conclude that by activating SA‐signalling whitefly feeding suppresses direct, JA‐based defences, but that parasitoids can adapt to this by exploiting specific, SA‐induced volatile emissions for host location.

Our work further confirms that herbivory contributes to selective pressure governing the evolution of inducible volatile signals as indirect plant defences.
Clinical markers in Italian‐speaking children with and without specific language impairment: a study of non‐word and real word repetition as predictors of grammatical ability
Authors: Dispaldro Marco , Leonard Laurence B. , Deevy Patricia 
Published: July 2013

AbstractBackgroundIn many languages a weakness in non‐word repetition serves as a useful clinical marker of specific language impairment (SLI) in children. However, recent work in Italian has shown that the repetition of real words may also have clinical utility. For young typically developing Italian children, real word repetition is more predictive of particular grammatical abilities than is non‐word repetition. This finding is important because these particular grammatical abilities—the production of present‐tense third‐person plural inflections and direct‐object clitic pronouns—are precisely those that are problematic for Italian‐speaking children with SLI. Along with their grammatical requirements, these two morpheme types present a significant phonological/prosodic challenge for these children.AimsTo replicate the findings with young typically developing Italian children and to determine whether real word repetition is also more predictive of the use of these two morpheme types than is non‐word repetition in a group of Italian‐speaking children with SLI.Methods & ProceduresSeventeen Italian‐speaking children with SLI and 17 younger typically developing children matched for mean length of utterance participated in tasks of real word and non‐word repetition as well as tasks requiring the production of direct‐object clitic pronouns and present‐tense third‐person plural inflections.Outcomes & ResultsChildren with SLI were less accurate than their younger peers on all measures. Importantly, for the younger typically developing children, real word repetition explained a significant amount of variance in the use of third‐person plural inflections and direct‐object clitic pronouns. For the children with SLI, in contrast, non‐word repetition was a significant predictor, whereas real word repetition was not a contributing factor.Conclusions & ImplicationsIt is argued that in Italian SLI, the grammatical details showing the greatest weakness present phonological/prosodic obstacles as well as grammatical challenges to these children. Consequently, non‐word repetition emerges as a predictor of these grammatical weaknesses in SLI, unlike the profile observed in typically developing Italian children.
Not all election winners are equal: Satisfaction with democracy and the nature of the vote
Authors: Singh Shane P. 
Published: July 2013

AbstractIt is well known that individuals who voted for the winning party in an election tend to be more satisfied with democracy than those who did not. However, many winners deviate from their first choice when voting. It is argued in this article that the mechanisms that engender satisfaction operate less forcefully among such winners, thereby lessening the impact of victory on satisfaction. Results show that the gap in satisfaction over electoral losers among these ‘non‐optimal winners’ is, in fact, much smaller than that of ‘optimal winners’, who voted in line with their expressed preferences. A win matters more for those who have a bigger stake in victory. The article further explores how the effect of optimal victory on satisfaction varies across electoral systems.
Geographic Disparities in Mammography Capacity in the South: A Longitudinal Assessment of Supply and Demand
Authors: Eberth Jan M. , Eschbach Karl , Morris Jeffrey S. , Nguyen Hoang T. , Hossain Md Monir , Elting Linda S. 
Published: July 2013

ObjectiveStudies have shown that there is sufficient availability of mammography; however, little is known about geographic variation in capacity. The purpose of this study was to determine the locations and extent of over/undersupply of mammography in 14 southern states from 2002 to 2008.Data SourcesMammography facility data were collected from the U.S. Food and Drug Administration (FDA). Population estimates, used to estimate the potential demand for mammography, were obtained from GeoLytics Inc.Study DesignUsing the two‐step floating catchment area method, we calculated spatial accessibility at the block group level and categorized the resulting index to represent the extent of under/oversupply relative to the potential demand.Principal FindingsResults show decreasing availability of mammography over time. The extent of over/undersupply varied significantly across the South. Reductions in capacity occurred primarily in areas with an oversupply of machines, resulting in a 68 percent decrease in the percent of women living in excess capacity areas from 2002 to 2008. The percent of women living in poor capacity areas rose by 10 percent from 2002 to 2008.ConclusionsOur study found decreasing mammography availability and capacity over time, with substantial variation across states. This information can assist providers and policy makers in their business planning and resource allocation decisions.
Validity of Infant Race/Ethnicity from Birth Certificates in the Context of U.S. Demographic Change
Authors: Mason Lisa Reyes , Nam Yunju , Kim Youngmi 
Published: July 2013

ObjectiveTo compare infant race/ethnicity based on birth certificates with parent report of infant race/ethnicity in a survey.Data SourcesThe 2007 Oklahoma birth certificates and SEED for Oklahoma Kids baseline survey.Study DesignUsing sensitivity scores and positive predictive values, we examined consistency of infant race/ethnicity across two data sources (N = 2,663).Data Collection/Extraction MethodsWe compared conventional measures of infant race/ethnicity from birth certificate and survey data. We also tested alternative measures that allow biracial classification, determined from parental information on the infant's birth certificate or parental survey report.Principal FindingsSensitivity of conventional measures is highest for whites and African Americans and lowest for Hispanics; positive predictive value is highest for Hispanics and African Americans and lowest for American Indians. Alternative measures improve values among whites but yield mostly low values among minority and biracial groups.ConclusionsHealth disparities research should consider the source and validity of infant race/ethnicity data when creating sampling frames or designing studies that target infants by race/ethnicity. The common practice of assigning the maternal race/ethnicity as infant race/ethnicity should continue to be challenged.
Partial and Incremental PCMH Practice Transformation: Implications for Quality and Costs
Authors: Paustian Michael L. , Alexander Jeffrey A. , El Reda Darline K. , Wise Chris G. , Green Lee A. , Fetters Michael D. 
Published: July 2013

ObjectiveTo examine the associations between partial and incremental implementation of the Patient Centered Medical Home (PCMH) model and measures of cost and quality of care.Data SourceWe combined validated, self‐reported PCMH capabilities data with administrative claims data for a diverse statewide population of 2,432 primary care practices in Michigan. These data were supplemented with contextual data from the Area Resource File.Study DesignWe measured medical home capabilities in place as of June 2009 and change in medical home capabilities implemented between July 2009 and June 2010. Generalized estimating equations were used to estimate the mean effect of these PCMH measures on total medical costs and quality of care delivered in physician practices between July 2009 and June 2010, while controlling for potential practice, patient cohort, physician organization, and practice environment confounders.Principal FindingsBased on the observed relationships for partial implementation, full implementation of the PCMH model is associated with a 3.5 percent higher quality composite score, a 5.1 percent higher preventive composite score, and $26.37 lower per member per month medical costs for adults. Full PCMH implementation is also associated with a 12.2 percent higher preventive composite score, but no reductions in costs for pediatric populations. Incremental improvements in PCMH model implementation yielded similar positive effects on quality of care for both adult and pediatric populations but were not associated with cost savings for either population.ConclusionsEstimated effects of the PCMH model on quality and cost of care appear to improve with the degree of PCMH implementation achieved and with incremental improvements in implementation.
Palmitate induces interleukin‐8 expression in human aortic vascular smooth muscle cells via Toll‐like receptor 4/nuclear factor‐κB pathway (TLR4/NF‐κB通路介导了软脂酸诱导人主动脉血管平滑肌细胞白细胞介素‐8的基因表达)
Authors: Quan Jinxing , Liu Jing , Gao Xiaobo , Liu Juxiang , Yang Haijing , Chen Wei , Li Weihua , Li Yonghong , Yang Weiguo , Wang Baoli 
Published: July 2013

AbstractBackgroundRecent evidence demonstrates that saturated free fatty acids (FFAs) induce the inflammatory response via the Toll‐like receptor 4 (TLR4) pathway. Interleukin‐8 (IL‐8) is a proinflammatory cytokine that induces vascular smooth muscle cell proliferation and migration in vitro. However, the regulation of IL‐8 expression by palmitate in human vascular smooth muscle cells (HVSMCs) has not been clarified. The aim of this study was to investigate the regulation of IL‐8 expression by free fatty acids and determine the underlying mechanisms in HVSMCs.MethodsHuman vascular smooth muscle cells were cultured and treated with palmitate, various signaling inhibitors or TLR4 shRNA adenovirus, and the mRNA and protein expression levels of IL‐8, nuclear factor κB (NF‐κB) luciferase activity and NF‐κB p65 binding activity were studied.ResultsPalmitate induced IL‐8 mRNA expression and secretion in a dose‐dependent manner. Palmitate significantly stimulated both nuclear factor κB (NF‐κB) luciferase activity and NF‐κB p65 binding activity, which were markedly diminished by pretreatment with the NF‐κB inhibitor, parthenolide. Parthenolide pretreatment also abolished IL‐8 mRNA and protein induction by palmitate. By contrast, disrupting the ceramide and phosphoinositide‐3 kinase (PI3K) pathways with myriocin and wortmannin did not affect palmitate‐induced IL‐8 expression. Inhibition of protein kinase C (PKC) activation with calphostin C and chelerythrine partially suppressed palmitate‐stimulated IL‐8 expression, but it had no effect on palmitate‐induced NF‐κB activation. Finally, knockdown of TLR4 markedly abolished palmitate‐induced NF‐κB activation and IL‐8 expression.ConclusionsPalmitate induces IL‐8 gene expression in HVSMCs through the TLR4/NF‐κB pathway.
Timely diagnosis of pulmonary artery tumor embolism by ultrasound‐guided transbronchial needle aspiration
Authors: Lee Seung Jun , Lee Jinwoo , Yu Su Jong , Lee Hyun Ju , Kim Kyung Ju , Lee Kyoung‐Bun , Park Young Sik 
Published: July 2013

AbstractPulmonary artery tumor embolism (PATE) is a rare disease without an established diagnostic method. In an autopsy series, however, the incidence of PATE was relatively high, between 3% and 26% in patients with a solid tumor. Here we report a case of a patient with a massive PATE from hepatocellular carcinoma diagnosed safely and promptly by endobronchial ultrasound‐guided transbronchial needle aspiration.