bluuebunny/crossref_metadata_2025 huggingface dataset:
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
Authors: Peng Yu , Leung Henry C. M. , Yiu S. M. , Chin Francis Y. L.
Published: April 2012

Motivation: Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from different species are highly uneven. Most existing genome assemblers usually have an assumption that sequencing depths are even. These assemblers fail to construct correct long contigs.

Results: We introduce the IDBA-UD algorithm that is based on the de Bruijn graph approach for assembling reads from single-cell sequencing or metagenomic sequencing technologies with uneven sequencing depths. Several non-trivial techniques have been employed to tackle the problems. Instead of using a simple threshold, we use multiple depthrelative thresholds to remove erroneous k-mers in both low-depth and high-depth regions. The technique of local assembly with paired-end information is used to solve the branch problem of low-depth short repeat regions. To speed up the process, an error correction step is conducted to correct reads of high-depth regions that can be aligned to highconfident contigs. Comparison of the performances of IDBA-UD and existing assemblers (Velvet, Velvet-SC, SOAPdenovo and Meta-IDBA) for different datasets, shows that IDBA-UD can reconstruct longer contigs with higher accuracy.

Availability: The IDBA-UD toolkit is available at our website http://www.cs.hku.hk/~alse/idba_ud

Contact:  chin@cs.hku.hk
CheShift-2: graphic validation of protein structures
Authors: Martin Osvaldo A. , Vila Jorge A. , Scheraga Harold A.
Published: April 2012

Summary: The differences between observed and predicted 13Cα chemical shifts can be used as a sensitive probe with which to detect possible local flaws in protein structures. For this reason, we previously introduced CheShift, a Web server for protein structure validation. Now, we present CheShift-2 in which a graphical user interface is implemented to render such local flaws easily visible. A series of applications to 15 ensembles of conformations illustrate the ability of CheShift-2 to locate the main structural flaws rapidly and accurately on a per-residue basis. Since accuracy plays a central role in CheShift predictions, the treatment of histidine (His) is investigated here by exploring which form of His should be used in CheShift-2.

Availability:  CheShift-2 is free of charge for academic use and can be accessed from www.cheshift.com

Contact:  has5@cornell.edu; jv84@cornell.edu

Supplementary information:  Supplementary data are available at the Bioinformatics online.
Ranking viruses: measures of positional importance within networks define core viruses for rational polyvalent vaccine development
Authors: Anderson Tavis K. , Laegreid William W. , Cerutti Francesco , Osorio Fernando A. , Nelson Eric A. , Christopher-Hennings Jane , Goldberg Tony L.
Published: April 2012

Motivation: The extraordinary genetic and antigenic variability of RNA viruses is arguably the greatest challenge to the development of broadly effective vaccines. No single viral variant can induce sufficiently broad immunity, and incorporating all known naturally circulating variants into one multivalent vaccine is not feasible. Furthermore, no objective strategies currently exist to select actual viral variants that should be included or excluded in polyvalent vaccines.

Results: To address this problem, we demonstrate a method based on graph theory that quantifies the relative importance of viral variants. We demonstrate our method through application to the envelope glycoprotein gene of a particularly diverse RNA virus of pigs: porcine reproductive and respiratory syndrome virus (PRRSV). Using distance matrices derived from sequence nucleotide difference, amino acid difference and evolutionary distance, we constructed viral networks and used common network statistics to assign each sequence an objective ranking of relative ‘importance’. To validate our approach, we use an independent published algorithm to score our top-ranked wild-type variants for coverage of putative T-cell epitopes across the 9383 sequences in our dataset. Top-ranked viruses achieve significantly higher coverage than low-ranked viruses, and top-ranked viruses achieve nearly equal coverage as a synthetic mosaic protein constructed in silico from the same set of 9383 sequences.

Conclusion: Our approach relies on the network structure of PRRSV but applies to any diverse RNA virus because it identifies subsets of viral variants that are most important to overall viral diversity. We suggest that this method, through the objective quantification of variant importance, provides criteria for choosing viral variants for further characterization, diagnostics, surveillance and ultimately polyvalent vaccine development.

Contact:  tgoldberg@vetmed.wisc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
RFMapp: ribosome flow model application
Authors: Zur Hadas , Tuller Tamir
Published: April 2012

Summary: The RFMapp is a graphical user interface application based on the RFM (ribosome flow model), enabling the estimation of the translation elongation rates of messenger ribonucleic acids (mRNAs) and the profile of ribosomal densities along the mRNAs, in a computationally efficient way. The RFMapp is based on the approach previously described by Reuveni et al., and unlike other traditional approaches in the field, which are mainly related to the genes' mean codon translation efficiency, the RFM additionally considers the codon order, the ribosomes' size and their order. Thus, it has been shown that RFM outperforms traditional predictors when analyzing both heterologous and endogenous genes.

Availability and implementation: Distributable cross-platform application and guideline are available for download at: http://www.cs.tau.ac.il/~tamirtul/RFM_Installers/install.htm

Contact:  tamirtul@post.tau.ac.il
Idiopathic scoliosis
Authors: Fairbank Jeremy
Published: April 2012

♦ Idiopathic scoliosis is the most common type of scoliosis

♦ It affects predominantly adolescent females

♦ Management depends on severity, cosmesis, and prognosis.
pFiD188, the Linear Virulence Plasmid of Rhodococcus fascians D188
Authors: Francis Isolde , De Keyser Annick , De Backer Philippe , Simón-Mateo Carmen , Kalkus Jutta , Pertry Ine , Ardiles-Diaz Wilson , De Rycke Riet , Vandeputte Olivier M. , El Jaziri Mondher , Holsters Marcelle , Vereecke Danny
Published: April 2012

Rhodococcus fascians is currently the only phytopathogen of which the virulence genes occur on a linear plasmid. To get insight into the origin of this replicon and into the virulence strategy of this broad-spectrum phytopathogen, the sequence of the linear plasmid of strain D188, pFiD188, was determined. Analysis of the 198,917 bp revealed four syntenic regions with linear plasmids of R. erythropolis, R. jostii, and R. opacus, suggesting a common origin of these replicons. Mutational analysis of pFi_086 and pFi_102, similar to cutinases and type IV peptidases, respectively, showed that conserved region R2 was involved in plasmid dispersal and pointed toward a novel function for actinobacterial cutinases in conjugation. Additionally, pFiD188 had three regions that were unique for R. fascians. Functional analysis of the stk and nrp loci of regions U2 and U3, respectively, indicated that their role in symptom development was limited compared with that of the previously identified fas, att, and hyp virulence loci situated in region U1. Thus, pFiD188 is a typical rhodococcal linear plasmid with a composite structure that encodes core functions involved in plasmid maintenance and accessory functions, some possibly acquired through horizontal gene transfer, implicated in virulence and the interaction with the host.
Protective effect of the maternally derived porcine circovirus type 2 (PCV2)-specific cellular immune response in piglets by dam vaccination against PCV2 challenge
Authors: Oh Yeonsu , Seo Hwi Won , Han Kiwon , Park Changhoon , Chae Chanhee
Published: April 2012

The objective of the present study was to evaluate (i) the passive transfer of maternally derived functional porcine circovirus type 2 (PCV2)-specific lymphocytes of seronegative sows immunized with the PCV2 vaccine to newborn piglets and (ii) the functional role of the maternally derived PCV2-specific cellular immune response in protecting newborn piglets from challenge with PCV2. After ingesting colostrums, piglets from vaccinated sows (PT01 and PT02) have significantly higher numbers of PCV2-specific gamma interferon-secreting cells, an increased PCV2-specific delayed type hypersensitivity response, and a stronger proliferative response of peripheral blood mononuclear cells compared with piglets from non-vaccinated seronegative sows (PT03 and PT04). In the PCV2 challenge study, the number of serum genomic PCV2 copies was significantly less in piglets from vaccinated sows (PT02) compared with piglets from non-vaccinated sows (PT04) at 7–28 days post-inoculation (P<0.05 and P<0.001). The histopathological lesions and immunohistochemical scores were significantly lower in piglets of vaccinated sows compared with those of non-vaccinated sows. To our knowledge, this is the first report of transferring a maternally derived PCV2-specific cellular immune response from vaccinated dams to their offspring. Maternally derived adaptive cellular immune responses play a critical role in protecting newborn piglets challenged with PCV2 at 3 weeks of age.
Chronic wasting disease and atypical forms of bovine spongiform encephalopathy and scrapie are not transmissible to mice expressing wild-type levels of human prion protein
Authors: Wilson Rona , Plinston Chris , Hunter Nora , Casalone Cristina , Corona Cristiano , Tagliavini Fabrizio , Suardi Silvia , Ruggerone Margherita , Moda Fabio , Graziano Silvia , Sbriccoli Marco , Cardone Franco , Pocchiari Maurizio , Ingrosso Loredana , Baron Thierry , Richt Juergen , Andreoletti Olivier , Simmons Marion , Lockey Richard , Manson Jean C. , Barron Rona M.
Published: April 2012

The association between bovine spongiform encephalopathy (BSE) and variant Creutzfeldt–Jakob disease (vCJD) has demonstrated that cattle transmissible spongiform encephalopathies (TSEs) can pose a risk to human health and raises the possibility that other ruminant TSEs may be transmissible to humans. In recent years, several novel TSEs in sheep, cattle and deer have been described and the risk posed to humans by these agents is currently unknown. In this study, we inoculated two forms of atypical BSE (BASE and H-type BSE), a chronic wasting disease (CWD) isolate and seven isolates of atypical scrapie into gene-targeted transgenic (Tg) mice expressing the human prion protein (PrP). Upon challenge with these ruminant TSEs, gene-targeted Tg mice expressing human PrP did not show any signs of disease pathology. These data strongly suggest the presence of a substantial transmission barrier between these recently identified ruminant TSEs and humans.
Inbreeding and inbreeding depression of early life traits in a cooperative mammal
Authors: NIELSEN JOHANNA F. , ENGLISH SINEAD , GOODALL‐COPESTAKE WILL P. , WANG JINLIANG , WALLING CRAIG A. , BATEMAN ANDREW W. , FLOWER TOM P. , SUTCLIFFE ROBERT L. , SAMSON JAMIE , THAVARAJAH NATHAN K. , KRUUK LOESKE E. B. , CLUTTON‐BROCK TIM H. , PEMBERTON JOSEPHINE M.
Published: April 2012

Mating between relatives often results in negative fitness consequences or inbreeding depression. However, the expression of inbreeding in populations of wild cooperative mammals and the effects of environmental, maternal and social factors on inbreeding depression in these systems are currently not well understood. This study uses pedigree‐based inbreeding coefficients from a long‐term study of meerkats (Suricata suricatta) in South Africa to reveal that 44% of the population have detectably non‐zero (F > 0) inbreeding coefficients. 15% of these inbred individuals were the result of moderate inbreeding (F ≥ 0.125), although such inbreeding events almost solely occurred when mating individuals had no prior experience of each other. Inbreeding depression was evident for a range of traits: pup mass at emergence from the natal burrow, hind‐foot length, growth until independence and juvenile survival. However, we found no evidence of significant inbreeding depression for skull and forearm length or for pup survival. This research provides a rare investigation into inbreeding in a cooperative mammal, revealing high levels of inbreeding, considerable negative consequences and complex interactions with the social environment.
A phylogeographic investigation of the hybrid origin of a species of swordtail fish from Mexico
Authors: JONES JULIA C. , PEREZ‐SATO JUAN‐ANTONIO , MEYER AXEL
Published: April 2012

Hybrid speciation may contribute significantly to generating biodiversity, but only a few well‐documented examples for it exist so far that do not involve polyploidization as a mechanism. The swordtail fish,Xiphophorus clemenciae, shows common hallmarks of a hybrid origin and still overlaps in its current geographic distribution with its putative ancestral species (Xiphophorus helleriiandXiphophorus maculatus).Xiphophorus clemenciaeprovides an ideal system for investigating the possible continued genetic interactions between a hybrid and its parental species. Here, we use microsatellite and mitochondrial markers to investigate the population structure of these species of swordtails and search for signs of recent hybridization. Individuals were sampled from 21 localities across the known range ofX. clemenciae– the Isthmus of Tehuantepec (IT) Mexico, and several environmental parameters that might represent barriers to dispersal were recorded. The hybridization event that gave rise toX. clemenciaeappears to be rather ancient, and a single origin is likely. We find negligible evidence for ongoing hybridization and introgression between the putative ancestral species, because they now occupy distinct ecological niches, and a common haplotype is shared by most populations ofX. clemenciae. The population structure within these species shows an isolation‐by‐distance (IBD) pattern and genetic differentiation between most populations is significant and high. We infer that tectonic evolution in the Isthmus has greatly restricted gene flow between the southern and central IT populations ofX. clemenciaeandX. helleriiiand provide preliminary information to aid in conservation management of this geographically restricted hybrid species,X. clemenciae.
Molecular phylogenies reveal host‐specific divergence of Ophiocordyceps unilateralis sensu lato following its host ants
Authors: KOBMOO N. , MONGKOLSAMRIT S. , TASANATHAI K. , THANAKITPIPATTANA D. , LUANGSA‐ARD J. J.
Published: April 2012

Ophiocordyceps unilateralis (Hypocreales, Ascomycetes) is an entomopathogenic fungus specific to formicine ants (Formicinae, Hymenoptera). Previous works have shown that the carpenter ant Camponotus leonardi acts as the principal host with occasional infections of ants from the genus Polyrhachis (sister genus of Camponotus). Observations were made on the permanent plots of Mo Singto, Khao Yai National Park of Thailand according to which O. unilateralis was found to occur predominantly on three host species: C. leonardi, C. saundersi and P. furcata. Molecular phylogenies of the elongation factor 1‐α and β‐Tubulin genes indicate a separation of O. unilateralis samples into three clades, reflecting specificity to each of the three different ant species. Samples collected from P. furcata and from C. leonardi were found to form sister groups with samples from C. saundersi forming an outgroup to the latter. Additional samples collected from unidentified ant species of Camponotus and Polyrhachis were positioned as outgroups to those samples on identified species. These results demonstrate that O. unilateralis is clearly not a single phylogenetic species and comprises at least three species that are specific to different host ant species. These cryptic species may arise through recent events of speciation driven by their specificity to host ant species.
Purification and biochemical characterization of functional complement factor H from human plasma fractions
Authors: Brandstätter H. , Schulz P. , Polunic I. , Kannicht C. , Kohla G. , Römisch J.
Published: April 2012

Background and Objectives  Complement factor H (CFH) acts as major regulator of the alternative pathway of complement and its mutations and polymorphisms predispose to various human diseases. We aimed to develop a scalable purification process of CFH from human plasma fractions to supply a pathogen‐safe and functional CFH concentrate.

Materials and Methods  Starting with intermediates of cold ethanol fractionation of plasma, CFH purification was performed with three chromatographic steps including solvent detergent treatment and nanofiltration. CFH functionality was tested by a haemolysis assay using sheep erythrocytes, by determining decay acceleration activity on C3 convertases and cofactor activity of C3b cleavage. CFH identity was confirmed by Western blot and mass spectrometry.

Results  Three scalable chromatographic steps highly purified full‐length and native CFH from human plasma fractions. The purification process enabled the removal of truncated and dysfunctional CFH species, yielding a native CFH concentrate as demonstrated in sensitive functional in vitro assays.

Conclusion  This novel process provides a pathogen‐safe and functional CFH concentrate that can be produced on an industrial scale and is suitable for pre‐/clinical studies.
Display Behavior and Habitat Use in Single and Mixed Populations of Anolis carolinensis and Anolis sagrei Lizards
Authors: Edwards Jessica R. , Lailvaux Simon P.
Published: April 2012

Introduced species can have a variety of effects on the behavior and ecology of native species. We compared display behavior and habitat use of introduced Anolis sagrei and native Anolis carolinensis lizards across three sites in Southern Louisiana. The chosen sites were similar in that they were all located in urban settings with clumped vegetation. The first site contained only A. sagrei, the second supported sympatric A. sagrei and A. carolinensis populations, and the third site harbored only A. carolinensis. We found that (1) A. carolinensis perched significantly higher when A. sagrei was present, consistent with previous studies, whereas perch height of A. sagrei was not altered by the presence of A. carolinensis; (2) A. carolinensis in single and mixed sites exhibited different proportions of display types, with individuals at the mixed Tulane site performing significantly more C displays than those at the single site; and (3) Anolis sagrei at the Tulane mixed site exhibited less push‐ups than those in the site with A. sagrei alone. These data suggest that the arrival of congeners can affect display behavior of anoles, although such effects are different for the natives and the invaders.
Next‐generation sequencing for mitochondrial diseases: A wide diagnostic spectrum
Authors: Vasta Valeria , Merritt II J Lawrence , Saneto Russell P. , Hahn Si Houn
Published: April 2012

Background:  The current diagnostic approach for mitochondrial disorders requires invasive procedures such as muscle biopsy and multiple biochemical testing but the results are often inconclusive. Clinical sequencing tests are available only for a limited number of genes. Recently, massively parallel sequencing has become a powerful tool for testing genetically heterogeneous conditions such as mitochondrial disorders.

Methods:  Targeted next‐generation sequencing was performed on 26 patients with known or suspected mitochondrial disorders using in‐solution capture for the exons of 908 known and candidate nuclear genes and an Illumina genome analyzer.

Results:  None of the 18 patients with various abnormal respiratory chain complex (RCC) activities had molecular defects in either subunits or assembly factors of mitochondrial RCC enzymes except a reference control sample with known mutations in SURF1. Instead, several variants in known pathogenic genes including CPT2, POLG, PDSS1, UBE3A, SDHD, and a few potentially pathogenic variants in candidate genes such as MTO1 or SCL7A13 were identified.

Conclusions:  Sequencing only nuclear genes for RCC subunits and assembly factors may not provide the diagnostic answers for suspected patients with mitochondrial disorders. The present findings indicate that the diagnostic spectrum of mitochondrial disorders is much broader than previously thought, which could potentially lead to misdiagnosis and/or inappropriate treatment. Overall analytic sensitivity and precision appear acceptable for clinical testing. Despite the limitations in finding mutations in all patients, the present findings underscore the considerable clinical benefits of targeted next‐generation sequencing and serve as a prototype for extending the clinical evaluation in this clinically heterogeneous patient group.
Temporal coincidence of environmental stress events modulates predation rates
Authors: Pincebourde Sylvain , Sanford Eric , Casas Jérôme , Helmuth Brian
Published: April 2012

Ecology Letters (2012) 15: 680–688

Climate warming experiments generally test the ecological effects of constant treatments while neglecting the influence of more realistic patterns of environmental fluctuations. Thus, little is known regarding how the temporal interaction between multiple episodes of thermal stress influences biotic interactions. We measured the sensitivity of predation rate in an intertidal sea star to changing levels of temporal coincidence of underwater and aerial thermal stress events. In laboratory trials, we controlled for intensity, variance and temporal patterning of both underwater and aerial body temperature. Predation rate decreased as underwater and aerial thermal stress episodes became temporally non‐coincident, despite a similar intensity and variance among treatments. Experiments under constant conditions were a poor predictor of more complex environmental scenarios because of these strong temporal interactions. Such temporal interactions may be widespread in various ecosystems, suggesting a strong need for empirical studies and models that link environmental complexity, physiology, behaviour and species interactions.
Using global catch data for inferences on the world’s marine fisheries
Authors: Kleisner K , Zeller D , Froese R , Pauly D
Published: April 2012

Detailed stock assessments, including the estimation of the absolute biomass of the ‘stocks’ exploited by fisheries, are often viewed as the gold standard for indicators of their status. However, such stock assessments are not available for the overwhelming majority of exploited stocks and fisheries globally. This requires the development, testing and dissemination of other, less data‐demanding indicators for use throughout the world, for example, for comparing the status of fisheries between different maritime countries or large marine ecosystems. Stock status plots, initially developed by staff of the United Nations Food and Agriculture Organization to assess global fisheries, are reviewed here, and their most recent incarnation, which accounts for stock rebuilding, is found to provide a robust overview of fisheries and of the major trends besetting them.
‘Down with Big Brother!’ The End of ‘Corporate Culturalism’?
Authors: Fleming Peter
Published: April 2012

abstract

Hugh Willmott's classic 1993JMSarticle, ‘Strength is Ignorance; Freedom is Slavery’, has greatly influenced how we understand culture management. It draws parallel's with George Orwell'sNineteen Eighty‐Fourto reveal the totalitarian aspirations of ‘corporate culturalism’. While it is sometimes said that employee resistance is missing in Willmott's account, I argue that it is implicitly pervasive, prefiguring subsequent investigations of ‘micro‐emancipation’ in management studies. The recent waning of scholarly interest in this type of resistance, however, also points to the contemporary relevance of Willmott's analysis. Emergent forms of corporate regulation utilize ‘biopower’ rather than just cultural conformity, rendering micro‐emancipation inadequate, but inspiring other types of dissent.
Definite Article Reduction and The Obligatory Contour Principle in York English1
Authors: Roeder Rebecca V.
Published: April 2012

This paper provides a phonological explanation for an observed pattern of Definite Article Reduction (DAR) in the city of York, northeast Yorkshire, England. Following a pattern common among very high frequency function words in English, the vowel‐less reduced definite article variably attaches leftward as s clitic. The cliticised definite article is subsequently affaected by the Obligatory Contour Principle (OCP). The phonetic realisations accommodated by this explanation include a non‐glottalised variant that is perceptually a zero realisation. Sociolinguistic observations indicate that older speakers and more locally‐oriented young, working‐class men are most likely to have acquired the phonological subtleties of this pattern.
Correlation Pursuit: Forward Stepwise Variable Selection for Index Models
Authors: Zhong Wenxuan , Zhang Tingting , Zhu Yu , Liu Jun S.
Published: April 2012

A stepwise procedure, correlation pursuit (COP), is developed for variable selection under the sufficient dimension reduction framework, in which the response variable Y is influenced by the predictors X1,X2,…,Xp through an unknown function of a few linear combinations of them. Unlike linear stepwise regression, COP does not impose a special form of relationship (such as linear) between the response variable and the predictor variables. The COP procedure selects variables that attain the maximum correlation between the transformed response and the linear combination of the variables. Various asymptotic properties of the COP procedure are established and, in particular, its variable selection performance under a diverging number of predictors and sample size is investigated. The excellent empirical performance of the COP procedure in comparison with existing methods is demonstrated by both extensive simulation studies and a real example in functional genomics.
A Road to Classification in High Dimensional Space: The Regularized Optimal Affine Discriminant
Authors: Fan Jianqing , Feng Yang , Tong Xin
Published: April 2012

For high dimensional classification, it is well known that naively performing the Fisher discriminant rule leads to poor results due to diverging spectra and accumulation of noise. Therefore, researchers proposed independence rules to circumvent the diverging spectra, and sparse independence rules to mitigate the issue of accumulation of noise. However, in biological applications, often a group of correlated genes are responsible for clinical outcomes, and the use of the covariance information can significantly reduce misclassification rates. In theory the extent of such error rate reductions is unveiled by comparing the misclassification rates of the Fisher discriminant rule and the independence rule. To materialize the gain on the basis of finite samples, a regularized optimal affine discriminant (ROAD) is proposed. The ROAD selects an increasing number of features as the regularization relaxes. Further benefits can be achieved when a screening method is employed to narrow the feature pool before applying the ROAD method. An efficient constrained co-ordinate descent algorithm is also developed to solve the associated optimization problems. Sampling properties of oracle type are established. Simulation studies and real data analysis support our theoretical results and demonstrate the advantages of the new classification procedure under a variety of correlation structures. A delicate result on continuous piecewise linear solution paths for the ROAD optimization problem at the population level justifies the linear interpolation of the constrained co-ordinate descent algorithm.
Accountability for Delegated and Implementing Acts after the Treaty of Lisbon
Authors: Peers Steve , Costa Marios
Published: April 2012

The comitology regime, the committee‐based system developed as a mechanism for controlling the Commission's exercise of its powers to implement EU measures, has been subject to severe criticism on grounds of lack of accountability and transparency. The system has recently been fundamentally reformed by means of the new Implementing Acts Regulation, which came into force on 1 March 2011. This paper investigates whether the new rules are sufficient to remedy accountability deficits as regards implementing acts and concludes that as far as accountability to the Member States is concerned, their control powers have remained static. In addition, the new‐delegated acts procedure introduced by the Treaty of Lisbon grants the European Parliament (EP) more control powers, although the EP's gains are more modest than they might appear. This change has come at the cost of reduced control powers for Member States as well as lowered standards of transparency for the public.
Characterization of glucose homeostasis and lipid profile in adult, seizure‐free, epileptic patients in Asian population
Authors: Phabphal K. , Limapichat K. , Sathirapanya P. , Setthawatcharawanich S. , Geater A.
Published: April 2012

Background and purpose:  The most common prescribed antiepileptic drugs (AEDs), phenytoin and valproate, are potent enzyme inducers and inhibitors of the cytochrome P450 system, which interfere with lipid profile and glucose homeostasis. Studies on this topic have suffered from inadequate assessment of confounders and have rarely included glucose homeostasis and lipid profile as well as both enzyme inducers and inhibitors in the same study. We sought to determine whether these drugs had an effect on lipid profile and glucose homeostasis in Thai epileptic patients.

Methods:  We recruited 98 patients with epilepsy (45 taking phenytoin, 27 taking valproate, and 26 not taking any AED). Fasting blood samples were obtained to measure serum lipid, and glucose homeostasis was evaluated via the oral glucose tolerance test. We calculated the homeostasis model assessment index for each patient.

Results:  Our study revealed that CYP450 was induced by AEDs, and that patients on phenytoin had an increased mean value of serum total cholesterol, serum total triglycerides, and serum LDL cholesterol when compared with patients with epilepsy taking valproate and those taking no AEDs. No statistical significant difference was observed between patients taking valproate and patients taking no AEDs. In addition, patients with epilepsy taking phenytoin had higher fasting plasma glucose levels at fasting state than both those taking valproate and those taking no AEDs. Thirty percent of the patients taking phenytoin exhibited insulin resistance. We have found a negative correlation between log insulin sensitivity and log TG, but not high‐density lipoprotein (HDL).

Conclusion:  CYP450‐induced phenytoin produces significant amelioration in several serologic markers of atherosclerosis. These findings suggest that phenytoin may substantially increase the risk of vascular events.
Fools, Facilitators and Flexians: Academic Identities in Marketised Environments
Authors: Smith Katherine
Published: April 2012

Employing the interdisciplinary field of health inequalities as a case study, this paper draws on interviews to explore subjective accounts of academic identities. It finds widespread acceptance that academia is a market place in which research‐active careers require academics to function as entrepreneurs marketing ideas to funders. Beyond this, two contrasting aspirational identities emerged: academics seeking to work collaboratively with policy makers (‘policy facilitators’) and academics seeking to challenge dominant discourses (‘Shakespearean fools’). Most interviewees identified strongly with one or the other of these identities and few believed academia sufficiently supported their preference, although there was some consensus that recent changes were aiding ‘policy facilitator’ roles. In interviewees' accounts of trying to pursue ‘Shakespearean fool’ type roles in marketised environments, a further, chameleon‐like identity emerged (‘flexians’): academics producing malleable ideas that can be adapted for different audiences. In exploring these identities, the paper challenges the popular distinction between mode‐1 and mode‐2 research.
Academic Work in Canada: the Perceptions of Early‐Career Academics
Authors: Jones Glen , Weinrib Julian , Metcalfe Amy Scott , Fisher Don , Rubenson Kjell , Snee Iain
Published: April 2012

This paper analyses junior academic staff's (assistant professors) perceptions of academic work in a highly decentralised Canadian ‘system’. Drawing on recent work by the authors on Canadian university tenure processes and remuneration, the paper compares the perceptions of assistant professor respondents with senior (associate full professor) peers to the Canadian component of the Changing Academic Professions (CAP) survey. The analysis suggests that junior academic staff perceive the academic workplace as reasonably positive and supportive. In addition to relatively high levels of satisfaction, institutional support and remuneration, the findings suggest that there are minimal substantive differences in levels of work and work patterns between junior and more senior academic staff, a finding at odds with the general literature and common sentiment, which suggests junior staff work longer hours. The differences that do emerge appear to be more modest and nuanced than is popularly characterised.
Negotiating Academic Values, Professorial Responsibilities and Expectations for Accountability in Today's University
Authors: Meyer Luanna H.
Published: April 2012

This paper argues that it is reasonable to expect the professoriate, including full professors, to balance traditional academic values with external demands for accountability. Today's universities are characterised by increasing diversity, wider access to higher education, decreasing funding and greater oversight through quality assurance: professors have a particular responsibility to respond to these modern realities and expectations. The essay explores how the role of professors in supporting knowledge development and dissemination through research and teaching can be elaborated and enhanced to ensure that universities contribute to the social good. How well the professoriate responds to contemporary challenges within and beyond traditional academic interests will determine the future of universities, just as previous responses have contributed to their endurance as institutions for more than 900 years. The essay concludes with emphasis on how full professors in particular can promote their special role and responsibilities for supporting the ideal and idea of the university in today's world.
Nation, Separation and Threat: An Analysis of British Media Discourses on the European Union Treaty Reform Process*
Authors: HAWKINS BENJAMIN
Published: April 2012

This article examines the framing of the European Union in British media debates surrounding the negotiation of the Lisbon Treaty. As such, it analyzes the discursive context in which both citizens' attitudes and government policies towards the EU are formed. It identifies a predominant, Eurosceptic discourse that dictates the terrain on which wider debates about the EU are conducted. This discourse views the EU through the lens of the nation‐state and frames the relationship between the United Kingdom and the EU in terms of separation and threat. The United Kingdom is excluded from the EU mainstream, which works to undermine its interests.
Variation in body temperature is related to ambient temperature but not experimental manipulation of insulation in two small endotherms with different thermoregulatory patterns
Authors: Boyles J. G. , Smit B. , McKechnie A. E.
Published: April 2012

Maintaining a high and constant body temperature (T
b) is thought to enhance performance in endotherms, but such a thermoregulatory pattern is energetically expensive. Thus, some variation in T
b is probably universal among endotherms, and several recent attempts have been made to generalize the factors that should cause this variation. Two factors that may be closely tied to the thermoregulatory pattern expressed are the cost of thermoregulation and food availability. To test these predictions, we measured T
b of eastern rock elephant shrews (Elephantulus myurus; a traditionally defined heterotherm) and Namaqua rock mice (Micaelamys namaquensis; a homeotherm) in the field and under semi‐natural conditions after experimentally reducing insulation by shaving a patch of dorsal fur. After accounting for ambient temperature (T
a), there was no significant difference in the level of variation in T
b between shaven and unshaven elephant shrews. In rock mice, the increase in heat loss paradoxically led to decreased variation in T
b in the field, but no effect was evident in captivity. Furthermore, as predicted, both species displayed significantly less variation in T
b under semi‐natural conditions when given food ad libitum and predation risk involved with obtaining that food was low. Our results show that small mammals, both homeothermic and heterothermic, are capable of altering their thermoregulatory patterns in response to ecological conditions (e.g. rapid changes in food availability). However, increasing the cost of thermoregulation, at least as it was done in this experiment, does not appear to affect the expression of T
b as strongly as does T
a.
Who is entitled to ‘earn sovereignty'? Legitimacy and regime support in Abkhazia and Nagorno‐Karabakh
Authors: Berg Eiki , Mölder Martin
Published: April 2012

Abkhazia and Nagorno‐Karabakh are internationally unrecognised political entities, or so‐called de facto states, that have emerged as a result of the incomplete and contested state‐formation of their parent states and of the secessionist movements that emerged in the power vacuum of the post‐Soviet space. In addition to examining the conventional reliance on the self‐determination principle, usually followed by a call for international recognition (as often practised by emerging sovereigns), this article aims to survey whether these political entities have proved that they embody ‘rightful authority’ as such and whether they ‘have earned their sovereignty’. In other words, it attempts to examine the self‐determination claims in Abkhazia and Nagorno‐Karabakh based on legitimacy criteria that are widely accepted for liberal democratic societies using an analysis of the respective issues as they were represented in focus‐group discussions in these two regions.
DOMUS AUREA, THE ‘SALA DELLE MASCHERE’: CHEMICAL AND SPECTROSCOPIC INVESTIGATIONS ON THE FRESCO PAINTINGS
Authors: PARADISI A. , SODO A. , ARTIOLI D. , BOTTI A. , CAVEZZALI D. , GIOVAGNOLI A. , POLIDORO C. , RICCI M. A.
Published: April 2012

In this paper, data collected from the wall fresco paintings of room 114, called the ‘Sala delle maschere’, of the Domus Aurea in Rome is analysed. The chemical composition of the efflorescence is investigated by infrared spectroscopy. The colour palette is determined by means of EDXRF, Raman spectroscopy and visible reflectance spectroscopy. EDXRF has allowed an extensive mapping of the elements present in the pigments and plaster; whilst in‐situ Raman spectroscopy has been determinant for attributing the molecular composition of the pigments in a number of doubtful cases. Most pigments identified are typical of Imperial Roman fresco paintings (first to fourth centuries AD) (Ward‐Perkins 1981); more interestingly, we found evidence of fragments painted with Egyptian blue, which was normally used mostly in official rooms.
Lumbar Posterolateral Fusion Using Heparin‐Conjugated Fibrin for Sustained Delivery of Bone Morphogenic Protein‐2 in a Rabbit Model
Authors: Koo Ki Hyoung , Yeo Do Hyun , Ahn Jung Min , Kim Byung‐Soo , Kim Chang‐Sung , Im Gun‐Il
Published: April 2012

We had devised a heparin‐conjugated fibrin (HCF) system to deliver bone morphogenic proteins (BMPs) for a long‐term period to enhance bone regeneration. In the present study, we tested the effectiveness of the delivery system for spinal fusion in a rabbit model. A total of 15 rabbits underwent posterolateral lumbar spine fusion with BMP‐2 (50 µg per collagen sponge). The control group received only collagen sponges without BMP‐2, another group (short‐term delivery [SD] group) received collagen sponges filled with fibrin gel loaded with BMP‐2, and the third group (long‐term delivery [LD] group) received collagen sponges filled with HCF loaded with BMP‐2. All animals were euthanized 8 weeks after surgery, and the fusion was assessed by radiographs, manual palpation, computed tomography, and mechanical testing. The fusion rate was significantly higher in the LD group using HCF than in the SD group or in the control group. Biomechanical testing showed the tensile strength was also significantly higher in the LD group using HCF than in other groups. The HCF system can provide a good option for the delivery of BMP‐2 on posterolateral lumbar spine fusion.
“Tort Tales” and TV Judges: Amplifying, Modifying, or Countering the Antitort Narrative?
Authors: Wilson Joshua C. , Ackerman Erin
Published: April 2012

This article joins the debate about the popular pervasiveness of antitort and antilitigation attitudes by examining whether, and to what extent, antitort or antilitigation sentiment is present in the narratives about law offered by reality-based television judge shows. Given the persistent debate about tort reform and scholars' recognition of the role played in this debate by simplified narratives about the legal system, we analyze whether reality-based TV judge shows as a genre contribute to the creation and dissemination antitort and antilitigation sentiment. Earlier studies led us to hypothesize that TV judge shows would largely support the antitort and antilitigation narratives. After coding over 55 hours of such shows, however, we conclude that they do not adopt this narrative. Rather, these shows present a view of the civil law system that largely treats plaintiffs' claims as legitimate and showcases the majority of defendants as wrongdoers. In spite of this, we argue that the particular dramatic qualities of TV judge shows limit their potential to serve as a strong counternarrative to antitort and antilitigation stories.
The Fluid Jurisprudence of Israel's Emergency Powers: Legal Patchwork as a Governing Norm
Authors: Mehozay Yoav
Published: April 2012

Israel's long-standing state of emergency has had considerable bearing on the state's governance. Less known, but equally important, is the fact that Israel's legal system features several overlapping and incoherent emergency legal mechanisms that exist side by side. This article demonstrates that Israel's ever-shifting body of emergency law has been used to suit its governing authorities’ political ends. A chief goal has been to create flexibility in the application of law in order to systematically discriminate against Palestinians while maintaining a degree of legitimacy as a government by law. With these various emergency legal mechanisms available, Israel's governing officials can extend the authorities of discrete emergency regulations by mixing and matching laws or by moving freely from one legal mechanism to the next to serve desired ends. This article argues further that what may have started as a pragmatic solution quickly became programmatic and concerted. Thus, contrary to the conception that Israel's convoluted emergency jurisprudence is the accidental outcome of trying times, Israel's complex emergency jurisprudence is in fact a governing tool. This reality compels us to consider new analytical frameworks in which a state of emergency is an enduring condition. To this end, this article draws on the work of colonial law scholars. By analyzing jurisdictional complexity in contexts where emergency is dominant, these studies explain the political motivation for maintaining structured ambiguity.
Left Atrial Dissection after Left Ventricular Aneurysm Repair
Authors: Pisklak Paul V. , Tolpin Daniel A. , Youngblood Sloan C. , Collard Charles D. , Pan Wei
Published: April 2012

Left atrial (LA) dissection is an uncommon entity that occurs most often after mitral valve surgery. We present a case of a 52‐year‐old man who developed an LA dissection after repair of a postinfarction left ventricular (LV) aneurysm. Transesophageal echocardiography was used to establish the diagnosis of an LA dissection that almost completely occluded the LA, limiting LV filling and causing hemodynamic instability.
Seeing Past Parallel Play: Survey Measures of Collaboration in Disaster Situations
Authors: Robinson Scott E. , Gaddis Benjamin S.
Published: April 2012

The literature on the management of policy networks has expanded greatly in the past decade. In spite of this attention, no consensus has emerged on how to measure collaboration or even what constitutes collaboration. This article uses data from a postdisaster survey to compare some existing approaches to measuring collaboration. We analyze various survey‐based measures ranging from respondent‐defined collaboration to activity‐based or contact‐based measures. We recommend that scholars consider opportunity costs as a key component in differentiating between significant collaboration and basic coordination (or “parallel play”). Based on this opportunity cost approach, we consider the distinctiveness of disaster collaboration.
News Photographs and Environmental Agenda Setting
Authors: Jenner Eric
Published: April 2012

Who and what influences the issues that policymakers attend to is central to the question of how power is exercised in politics. This study builds upon research by Soroka that proposes an expanded model of agenda setting as a means to examine how the media influences issue salience for the public and policymakers. It expands on Soroka's model by investigating the hypothesis that photographic attention to environmental issues in the news media influences issue salience for the mass public and governmental decision makers. There is little research that substantiates the idea, but it is widely believed that photographs have influence on the policy agenda. I use a dynamic, multidirectional model to estimate whether the volume of news photographs, in addition to news stories, influences issue salience among the mass public and policymakers. Data are longitudinal and measures of attention are operationalized as the number of congressional committee meetings, concern for the environment as a “most important problem” in public opinion polls, environmental news stories in The New York Times, and environmental news photographs in Time magazine. Results suggest that photographic attention does influence environmental policy agenda dynamics in some counterintuitive ways that are distinct from the effects of the news stories. While news stories appear to increase public attention toward the environment, they have little influence on policymaker attention. News photographs, on the other hand, appear to drive congressional committee attention but elicit an ambivalent public response.