bluuebunny/crossref_metadata_2025 huggingface dataset:
Nanoporous Platinum Electrodes as Substrates for Metal Oxide-Supported Noble Metal Electrocatalytic Nanoparticles: Synergistic Effects During Electrooxidation of Ethanol
Authors: Rutkowska Iwona A. , Koster Margaretta D. , Blanchard Gary J. , Kulesza Pawel J.
Published: July 2014

Electrocatalytic oxidation of ethanol in acid medium (0.5 mol dm–3 H2SO4) was significantly enhanced by not only supporting bimetallic PtRu nanoparticles on nanostructured metal oxides (TiO2 or WO3), but also by depositing such catalytic systems on planar nanoporous platinized electrode substrates. Incorporation of TiO2 or WO3 into the electrocatalytic interface was likely to improve proton mobility and to provide –OH groups capable of inducing the removal of poisoning species, such as CO, from the Pt sites in the bimetallic PtRu catalyst. Synergistic interactions between ruthenium and titania were also possible. Regularly porous nanostructured platinum substrate also permitted development of submicro ‘reactors’ where reactant molecules, electrolyte ions, and all active components (TiO2 or WO3, Pt substrate, PtRu catalytic sites) could co-exist and become easily accessible. While WO3 was able to undergo fast reversible redox transitions to non-stoichiometric oxides, efficient utilization of inert (non-electroactive) TiO2 required admixing with carbon nanotubes to ensure easy charge distribution and good conductivity at the electrocatalytic interface.
lrgpr: interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R
Authors: Hoffman Gabriel E. , Mezey Jason G. , Schadt Eric E.
Published: July 2014

Summary:  The linear mixed model is the state-of-the-art method to account for the confounding effects of kinship and population structure in genome-wide association studies (GWAS). Current implementations test the effect of one or more genetic markers while including prespecified covariates such as sex. Here we develop an efficient implementation of the linear mixed model that allows composite hypothesis tests to consider genotype interactions with variables such as other genotypes, environment, sex or ancestry. Our R package, lrgpr, allows interactive model fitting and examination of regression diagnostics to facilitate exploratory data analysis in the context of the linear mixed model. By leveraging parallel and out-of-core computing for datasets too large to fit in main memory, lrgpr is applicable to large GWAS datasets and next-generation sequencing data.

Availability and implementation:  lrgpr is an R package available from lrgpr.r-forge.r-project.org

Contact:  gabriel.hoffman@mssm.edu

Supplementary information:   Supplementary data are available at Bioinformatics online.
Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data
Authors: Boeva Valentina , Popova Tatiana , Lienard Maxime , Toffoli Sebastien , Kamal Maud , Le Tourneau Christophe , Gentien David , Servant Nicolas , Gestraud Pierre , Rio Frio Thomas , Hupé Philippe , Barillot Emmanuel , Laes Jean-François
Published: July 2014

Motivation: Because of its low cost, amplicon sequencing, also known as ultra-deep targeted sequencing, is now becoming widely used in oncology for detection of actionable mutations, i.e. mutations influencing cell sensitivity to targeted therapies. Amplicon sequencing is based on the polymerase chain reaction amplification of the regions of interest, a process that considerably distorts the information on copy numbers initially present in the tumor DNA. Therefore, additional experiments such as single nucleotide polymorphism (SNP) or comparative genomic hybridization (CGH) arrays often complement amplicon sequencing in clinics to identify copy number status of genes whose amplification or deletion has direct consequences on the efficacy of a particular cancer treatment. So far, there has been no proven method to extract the information on gene copy number aberrations based solely on amplicon sequencing.

Results: Here we present ONCOCNV, a method that includes a multifactor normalization and annotation technique enabling the detection of large copy number changes from amplicon sequencing data. We validated our approach on high and low amplicon density datasets and demonstrated that ONCOCNV can achieve a precision comparable with that of array CGH techniques in detecting copy number aberrations. Thus, ONCOCNV applied on amplicon sequencing data would make the use of additional array CGH or SNP array experiments unnecessary.

Availability and implementation:  http://oncocnv.curie.fr/

Contact:  valentina.boeva@curie.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Clearing the Cupboard: The Role of Public Relations in London Clearing Banks’ Collective Legitimacy-Seeking, 1950–1980
Authors: Reveley James , Singleton John
Published: July 2014

This essay conceptualizes and historically documents a negle cted trade association function: legitimacy-seeking. It uses the Committee of London Clearing Bankers case to show how an association can, by using manipulative public relations techniques, fulfil that function for its members. To the circumstances that prevent rent-seeking associations from becoming industry level efficiency enhancers, the essay adds a new factor—a political legitimacy crisis. Through the Committee, the banks’ leaders responded to such a crisis in the 1970s prompted by the threat of bank nationalization. The case yields the following generalizable point. When members are faced with an external legitimacy threat, a trade association, even one with a history of collaborative learning, can get stuck at the rent-seeking end of the associational spectrum. By morphing from a cartel into merely a vehicle for asserting its members’ political legitimacy through instrumental public relations, this is just where the Committee remained on that continuum.
Star formation in shocked cluster spirals and their tails
Authors: Roediger E. , Brüggen M. , Owers M. S. , Ebeling H. , Sun M.
Published: July 2014

Recent observations of ram pressure stripped spiral galaxies in clusters revealed details of the stripping process, i.e. the truncation of all interstellar medium phases and of star formation (SF) in the disc, and multiphase star-forming tails. Some stripped galaxies, in particular in merging clusters, develop spectacular star-forming tails, giving them a jellyfish-like appearance. In merging clusters, merger shocks in the intracluster medium (ICM) are thought to have overrun these galaxies, enhancing the ambient ICM pressure and thus triggering SF, gas stripping, and tail formation. We present idealized hydrodynamical simulations of this scenario, including standard descriptions for SF and stellar feedback. To aid the interpretation of recent and upcoming observations, we focus on particular structures and dynamics in SF patterns in the remaining gas disc and in the near tails, which are easiest to observe. The observed jellyfish morphology is qualitatively reproduced for, both, face-on and edge-on stripping. In edge-on stripping, the interplay between the ICM wind and the disc rotation leads to asymmetries along the ICM wind direction and perpendicular to it. The apparent tail is still part of a highly deformed gaseous and young stellar disc. In both geometries, SF takes place in knots throughout the tail, such that the stars in the tails show no ordered age gradients. Significant SF enhancement in the disc occurs only at radii where the gas will be stripped in due course.
Intrinsic alignments in the cross-correlation of cosmic shear and cosmic microwave background weak lensing
Authors: Hall Alex , Taylor Andy
Published: July 2014

We demonstrate that the intrinsic alignment of galaxies with large-scale tidal fields sources an extra contribution to the recently detected cross-correlation of galaxy shear and weak lensing of the microwave background. The extra term is the analogy of the ‘GI’ term in standard cosmic shear studies, and results in a reduction in the amplitude of the cross-correlation. We compute the intrinsic alignment contribution in linear and non-linear theory, and show that it can be at roughly the 15 per cent level for the Canada–France–Hawaii Telescope Stripe 82 redshift distribution, if the canonical amplitude of intrinsic alignments is assumed. The new term can therefore potentially reconcile the apparently low value of the measured cross-correlation with standard Λ cold dark matter. We discuss various small-scale effects in the signal and the dependence on the source redshift distribution. We discuss the exciting possibility of self-calibrating intrinsic alignments with a joint analysis of cosmic shear and weak lensing of the microwave background.
Single-institution Experience of SBRT for Lung Metastases in Sarcoma Patients
Authors: Soyfer Viacheslav , Corn Benjamin W. , Shtraus Natan , Honig Nir , Meir Yaron , Kollender Jehuda , Merimsky Ofer
Published: July 2014

Objectives:

Lung metastasectomy is regarded as the standard procedure for improving the prognosis of patients with metastatic sarcoma. Few reports are available in the literature describing the value of stereotactic body radiation therapy (SBRT) of lung metastases from primary sarcoma as an alternative to surgical treatment. We therefore sought to expand the evidence base for this modality.

Materials and Methods:

Twenty-two patients with metastatic sarcoma to lung were treated by SBRT. The retrospective analysis of overall survival, toxicity, and local control of 53 treated lesions is presented in the study. Lung lesions were grouped into 2 categories for follow-up: <10 mm or ≥10 mm diameter.

Results:

Of 34 lesions <10 mm, 24 achieved complete response, 3 partial response, and 7 stable disease. The results of 18 lesions measuring >10 mm were as follows: 5 complete response, 5 progressive disease, and 8 stable disease. No progressive disease of all SBRT treated lesions was found at a median follow-up of 95 months (SD 32). Five-year overall survival of the entire group was 62% from the time of diagnosis and 50% from start of treatment. The treatment was well tolerated with minimal, mainly skin toxicity.

Conclusion:

SBRT is an effective tool that might be used as an alternative to operative treatment of lung metastases in sarcoma patients
The archaic chaperone–usher pathways may depend on donor strand exchange for intersubunit interactions
Authors: Wu Miaomiao , Xu Shihui , Zhu Wei , Mao Xiaohua
Published: July 2014

Subunit–subunit interactions of the classical and alternate chaperone–usher (CU) systems have been shown to proceed through a donor strand exchange (DSE) mechanism. However, it is not known whether DSE is required for intersubunit interactions in the archaic CU system. We have previously shown that the Myxococcus xanthus Mcu system, a member of the archaic CU family that functions in spore coat formation, is likely to use the principle of donor strand complementation to medicate chaperone–subunit interactions analogous to the classical CU pathway. Here we describe the results of studies on Mcu subunit–subunit interactions. We constructed a series of N-terminal-deleted, single amino acid-mutated and donor strand-complemented Mcu subunits, and characterized their abilities to participate in subunit–subunit interactions. It appears that certain residues in both the N and C termini of McuA, a subunit of the Mcu system, play a critical role in intersubunit interactions and these interactions may involve the general principle of DSE of the classical and alternate CU systems. In addition, the specificity of the M. xanthus CU system for Mcu subunits over other spore coat proteins is demonstrated.
Assessing allele specific expression across multiple tissues from RNA-seq read data
Authors: Pirinen Matti , Lappalainen Tuuli , Zaitlen Noah A. , Dermitzakis Emmanouil T. , Donnelly Peter , McCarthy Mark I. , Rivas Manuel A. ,   GTEx Consortium
Published: July 2014

Motivation:

RNA sequencing enables allele specific expression (ASE) studies that complement standard genotype expression studies for common variants and, importantly, also allow measuring the regulatory impact of rare variants. The Genotype-Tissue Expression project (GTEx) is collecting RNA-seq data on multiple tissues of a same set of individuals and novel methods are required for the analysis of these data.

Results:

We present a statistical method to compare different patterns of ASE across tissues and to classify genetic variants according to their impact on the tissue-wide expression profile. We focus on strong ASE effects that we are expecting to see for protein-truncating variants, but our method can also be adjusted for other types of ASE effects. We illustrate the method with a real data example on a tissue-wide expression profile of a variant causal for lipoid proteinosis, and with a simulation study to assess our method more generally.

Availability:

MAMBA software:http://birch.well.ox.ac.uk/∼rivas/mamba/R source code and data examples:http://www.iki.fi/mpirinen/

Contact:

matti.pirinen@helsinki.fi

rivas@well.ox.ac.uk
Genetic disruption of the core circadian clock impairs hippocampus-dependent memory
Authors: Wardlaw Sarah M. , Phan Trongha X. , Saraf Amit , Chen Xuanmao , Storm Daniel R.
Published: July 2014

Perturbing the circadian system by electrolytically lesioning the suprachiasmatic nucleus (SCN) or varying the environmental light:dark schedule impairs memory, suggesting that memory depends on the circadian system. We used a genetic approach to evaluate the role of the molecular clock in memory. Bmal1−/− mice, which are arrhythmic under constant conditions, were examined for hippocampus-dependent memory, LTP at the Schaffer-collateral synapse, and signal transduction activity in the hippocampus. Bmal1−/− mice exhibit impaired contextual fear and spatial memory. Furthermore, LTP in hippocampal slices from Bmal1−/− mice is also significantly decreased relative to that from wild-type mice. Activation of Erk1,2 MAP kinase (MAPK) during training for contextual fear memory and diurnal oscillation of MAPK activity and cAMP in the hippocampus is also lost in Bmal1−/− mice, suggesting that the memory defects are due to reduction of the memory consolidation pathway in the hippocampus. We conclude that critical signaling events in the hippocampus required for memory depend on BMAL1.
Transport of Boron by thetassel-less1Aquaporin Is Critical for Vegetative and Reproductive Development in Maize
Authors: Durbak Amanda R. , Phillips Kimberly A. , Pike Sharon , O’Neill Malcolm A. , Mares Jonathan , Gallavotti Andrea , Malcomber Simon T. , Gassmann Walter , McSteen Paula
Published: July 2014

The element boron (B) is an essential plant micronutrient, and B deficiency results in significant crop losses worldwide. The maize (Zea mays) tassel-less1 (tls1) mutant has defects in vegetative and inflorescence development, comparable to the effects of B deficiency. Positional cloning revealed that tls1 encodes a protein in the aquaporin family co-orthologous to known B channel proteins in other species. Transport assays show that the TLS1 protein facilitates the movement of B and water into Xenopus laevis oocytes. B content is reduced in tls1 mutants, and application of B rescues the mutant phenotype, indicating that the TLS1 protein facilitates the movement of B in planta. B is required to cross-link the pectic polysaccharide rhamnogalacturonan II (RG-II) in the cell wall, and the percentage of RG-II dimers is reduced in tls1 inflorescences, indicating that the defects may result from altered cell wall properties. Plants heterozygous for both tls1 and rotten ear (rte), the proposed B efflux transporter, exhibit a dosage-dependent defect in inflorescence development under B-limited conditions, indicating that both TLS1 and RTE function in the same biological processes. Together, our data provide evidence that TLS1 is a B transport facilitator in maize, highlighting the importance of B homeostasis in meristem function.
Critical quality factors for successful TQM implementation in Libyan oil and gas sector
Authors: Munir Ahmad Mohammad , Elhuni Redha
Published: July 2014

Purpose

– The purpose of this paper is to investigate quality factors that are absolutely essential for successful implementation of total quality management (TQM) in Libyan oil and gas companies (LOGCs).

Design/methodology/approach

– In all, 11 quality factors with 42 elements were identified to develop a questionnaire to carry out the survey in order to identify the quality factors that are seen by LOGCs to be critical to the success of TQM implementation. In total, 45 questionnaires were provided by hand to quality-related managers from the Libyan oil and gas sector. A total of 42 were returned sufficiently completed, that gave us a response rate of approximately 93.33 per cent.

Findings

– The empirical analysis demonstrates several key findings: the analysis indicated that 24 quality factors are found to be critical and absolutely essential for successful TQM implementation. These factors classify into three levels of criticality. All of the factors were found to be supported by similar studies and cited literatures.

Research limitations/implications

– The research is subject to the normal limitations of survey research. The study is using perceptual data provided by quality managers and engineers which may not provide clear picture. It may be suitable to consider gathering information from various stakeholders such as employees, customers, suppliers and even competitors. However, this can be overcome using multiple methods to collect data in future studies. Interestingly, the findings here may be generalisable outside Libya, i.e. South Mediterranean countries.

Practical implications

– LOGCs should consider TQM as an innovative tool for improving business performance in today's competitive environment. The findings suggest that the TQM critical success factors should be implemented completely as a whole package rather than on a fragmented basis to get the full potential of the TQM.

Originality/value

– The study investigate the critical quality factors for successful TQM implementation which will direct an organisation towards business excellence and enhancing success of TQM practices in the oil and gas sector. Very few studies have been performed to investigate and understand this issue. Therefore, the research can make a useful contribution.
An examination of the structure and dynamics of Singapore's maturing Central Area office market
Authors: Hin David Ho Kim , Rengarajan Satyanarain , Glascock John
Published: July 2014

Purpose

– The purpose of this paper is to examine the structure and dynamics of Singapore's Central Area office market. A long-run equilibrium relationship is tested and a short-run adjustment error correction model are estimated, incorporating appropriate serial error correction. The long-run equation is estimated for office rent, with office employment and available stock.

Design/methodology/approach

– With the vector error correction model (VECM), the lagged rent, available stock, office employment, vacancy and occupied stock (OS) can impact the rental adjustment process. Equilibrium rent on the whole reacts positively to lagged rents, available stock, office employment, OS and negatively to vacancy rates (VC). Past levels of positive change in VC and rental growth can have negative effects on current OS.

Findings

– While good economic conditions signaled by increases in rents increase the supply of new stock (available space), higher rents and VC dampen the long-term occupied space (space absorption) in accordance with economic theory. Available stock can be forecasted by past rent and absorption levels owing to the developer's profit-driven nature.

Research limitations/implications

– An understanding of the interaction between the macroeconomic variables and the Central Area office market is useful to domestic and foreign investors and developers, who then can better evaluate their decision making in commercial real estate investment and development projects.

Practical implications

– It is implicit that the Singapore Central Area office market requires at least a year before any rental increase can potentially dampen the space demanded. Firms are attracted to locate there owing to agglomeration economies and they are willing to pay premium office rents in conjunction with office space intensification in the Central Area. Newly built space is positively affected by past rents. Urban Redevelopment Authority and private real estate developers should be wary of excess office sector vacancies by avoiding over supply, even though an increase in the supply of office space in the Central Area can have a positive impact on office rent in the longer term. Most of the office space development would tend to meet the demand in the long run. Rental stickiness is exemplified as rental changes are affected by lagged rent.

Social implications

– Policy makers are better enabled to stabilize the office sectors of the real estate market if so required.

Originality/value

– The paper adopts the VECM and validated by empirical evidence, to investigate the long-run equilibrium relationship and short-term corrections underlying the dynamics of the Singapore Central office market. Delay in the restoration of equilibrium in real estate markets is attributed to factors like lease terms and supply lags.
Property investment decision making by Australian REITs
Authors: Parker David
Published: July 2014

Purpose

– The purpose of this paper is to investigate property investment decision making by Australian REITs.

Design/methodology/approach

– Through an extensive literature review, a normative model of the property investment decision-making process is proposed. Based on semi-structured interviews with senior Australian REIT decision makers, a descriptive model of the property investment decision-making process by Australian REITs is developed. The normative model and descriptive model are compared and a prescriptive model of the Australian REIT property investment decision-making process proposed.

Findings

– With the four stage, 20-step process proposed in the normative model found to be generally supported by the descriptive model developed, this may potentially comprise an effective prescriptive model for the Australian REIT property investment decision-making process.

Research limitations/implications

– Further research is required to investigate if the prescriptive model is generalisable across other property investment decision-making groups or over time and whether it may lead to “good” decisions.

Practical implications

– The prescriptive model proposed may contribute consistency and transparency to the decision-making process, if adopted by Australian REITs, potentially leading to better decisions.

Social implications

– Greater consistency and transparency in property investment decision making by Australian REITs may lead to the optimal allocation of capital and greater investor confidence in the sector.

Originality/value

– The findings comprise the first prescriptive model of the Australian REIT property investment decision-making process, forming a basis for comparative investigation of that process adopted by other property investment decision-making groups.
Corporate community responsibility as an outcome of individual embeddedness
Authors: Blombäck Anna , Wigren-Kristoferson Caroline
Published: July 2014

Purpose

– The purpose of this article is to improve our understanding of the nature of social responsibility in actual practices and, specifically, the influence of individuals on these processes.

Design/methodology/approach

– An abductive approach is applied (Alvesson and Sköldberg 1994), i.e. theory is developed by moving between theory and four empirical cases. The stories highlight the importance of the individual and closeness to local stakeholders and the presence of overlapping rationales.

Findings

– The individuals’ simultaneous roles – as owners, managers and community members – influence how they are held or see themselves as accountable and how they account for the firms’ engagement in the community. The activities are conducted in the name of the firm but originate from private as well as business-oriented concerns. Our conclusions encourage an extension of the corporate social responsibility (CSR) construct to approach it as an entangled phenomenon resulting from the firm and the individual embeddedness in internal and external cultures.

Originality/value

– This study brings the individual managers and owner-managers into focus and how their interplay with the surrounding context can create additional dimensions of accountability, which impact on the decisions taken in regard to CSR. A micro-perspective is applied. Corporate community responsibility, particularly in smaller and rural communities, contributes to recognize and understand how individuals influence and are influenced by CSR.
Corruption, governance and economic growth in Sub-Saharan Africa: a need for the prioritisation of reform policies
Authors: Omoteso Kamil , Ishola Mobolaji Hakeem
Published: July 2014

Purpose

– This study aims to investigate the impact of governance indices (especially control of corruption) on economic growth in some selected Sub-Sahara African (SSA) countries with a view to making policy recommendations. Specifically, the study attempts to assess whether either governance reforms (especially those relating to control of corruption) or simultaneous policy reforms could have any impact on the growth of the sample SSA countries.

Design/methodology/approach

– The governance indicators used in this study were drawn from the PRS Group and the Worldwide Governance Indicators for 2002-2009, while the real gross domestic product (GDP) per capita growth data were obtained from the World Bank database. The study covered 47 SSA countries, and it adopted the panel data framework, the fixed effect, the random effect and the maximum likelihood estimation techniques for the analyses.

Findings

– The study found that political stability and regulatory quality indicators have growth-enhancing features, as they impact on economic growth in the region significantly, while government effectiveness impacts negatively on economic growth in the region. Despite, several anti-corruption policies in the region, the impact of corruption control on economic growth is not very obvious. The study also found that simultaneous implementation of the voice and accountability and the rule of law indicators has more positive impact on economic growth in the region. Both policies are complementary, and, hence, can be pursued simultaneously.

Research limitations/implications

– The results suggest that reform efforts that aim at enhancing accountability, regulatory quality, political stability and the rule of law have more growth-enhancing features and, thus, should be given more priority over reform efforts that singly address the issue of control of corruption due to the endemic, systemic and ubiquitous nature of corruption in the region.

Practical implications

– The study suggests that reform efforts that aim at enhancing accountability, regulatory quality and rule of law have more growth-enhancing features and, therefore, should be given more priority.

Originality/value

– Many previous studies attempted to examine the impact of corruption on economies, but this paper tries to assess the effect of corruption control and other governance indices on economic growth in the most vulnerable region of the world, the SSA. Besides, the study adopts the panel data framework which makes it possible to allow for differences in the form of unobservable individual country effects.
Microbiology of sugar‐rich environments: diversity, ecology and system constraints
Authors: Lievens Bart , Hallsworth John E. , Pozo Maria I. , Belgacem Zouhaier Ben , Stevenson Andrew , Willems Kris A. , Jacquemyn Hans
Published: July 2014

Microbial habitats that contain an excess of carbohydrate in the form of sugar are widespread in the microbial biosphere. Depending on the type of sugar, prevailing water activity and other substances present, sugar‐rich environments can be highly dynamic or relatively stable, osmotically stressful, and/or destabilizing for macromolecular systems, and can thereby strongly impact the microbial ecology. Here, we review the microbiology of different high‐sugar habitats, including their microbial diversity and physicochemical parameters, which act to impact microbial community assembly and constrain the ecosystem. Saturated sugar beet juice and floral nectar are used as case studies to explore the differences between the microbial ecologies of low and higher water‐activity habitats respectively. Nectar is a paradigm of an open, dynamic and biodiverse habitat populated by many microbial taxa, often yeasts and bacteria such as, amongst many others, Metschnikowia spp. and Acinetobacter spp., respectively. By contrast, thick juice is a relatively stable, species‐poor habitat and is typically dominated by a single, xerotolerant bacterium (Tetragenococcus halophilus). A number of high‐sugar habitats contain chaotropic solutes (e.g. ethyl acetate, phenols, ethanol, fructose and glycerol) and hydrophobic stressors (e.g. ethyl octanoate, hexane, octanol and isoamyl acetate), all of which can induce chaotropicity‐mediated stresses that inhibit or prevent multiplication of microbes. Additionally, temperature,pH, nutrition, microbial dispersion and habitat history can determine or constrain the microbiology of high‐sugar milieux. Findings are discussed in relation to a number of unanswered scientific questions.
Measuring and explaining regulatory reform in the EU: A time‐series analysis of eight sectors, 1984–2012
Authors: Citi Manuele , Justesen Mogens K.
Published: July 2014

Over the last three decades, European Union regulation of the internal market has become highly pervasive, affecting practically all domains of European citizens' lives. Many studies have focused on understanding the process and causes of regulatory change, but with limited attempts to analyse the more general sources of regulatory reform. This article focuses on the determinants of stability and change in EU regulation. An original dataset of 169 pieces of legislation (regulations, directives and decisions) across eight different sectors is developed and the dynamics of regulatory reform in the EU are analysed. Using time‐series analysis of count data, evidence is found that the number of winning coalitions in the Council and the size of EU membership have a significant impact on regulatory reform in the EU. By contrast, the ideological composition of the EU's legislative bodies is not systematically related to regulatory reform.
DNA barcoding gap: reliable species identification over morphological and geographical scales
Authors: Čandek Klemen , Kuntner Matjaž
Published: July 2014

The philosophical basis and utility of DNA barcoding have been a subject of numerous debates. While most literature embraces it, some studies continue to question its use in dipterans, butterflies and marine gastropods. Here, we explore the utility of DNA barcoding in identifying spider species that vary in taxonomic affiliation, morphological diagnosibility and geographic distribution. Our first test searched for a ‘barcoding gap’ by comparing intra‐ and interspecific means, medians and overlap in more than 75 000 computed Kimura 2‐parameter (K2P) genetic distances in three families. Our second test compared K2P distances of congeneric species with high vs. low morphological distinctness in 20 genera of 11 families. Our third test explored the effect of enlarging geographical sampling area at a continental scale on genetic variability in DNA barcodes within 20 species of nine families. Our results generally point towards a high utility of DNA barcodes in identifying spider species. However, the size of the barcoding gap strongly depends on taxonomic groups and practices. It is becoming critical to define the barcoding gap statistically more consistently and to document its variation over taxonomic scales. Our results support models of independent patterns of morphological and molecular evolution by showing that DNA barcodes are effective in species identification regardless of their morphological diagnosibility. We also show that DNA barcodes represent an effective tool for identifying spider species over geographic scales, yet their variation contains useful biogeographic information.
Imputation of missing data in life‐history trait datasets: which approach performs the best?
Authors: Penone Caterina , Davidson Ana D. , Shoemaker Kevin T. , Di Marco Moreno , Rondinini Carlo , Brooks Thomas M. , Young Bruce E. , Graham Catherine H. , Costa Gabriel C.
Published: July 2014

Despite efforts in data collection, missing values are commonplace in life‐history trait databases. Because these values typically are not missing randomly, the common practice of removing missing data not only reduces sample size, but also introduces bias that can lead to incorrect conclusions. Imputing missing values is a potential solution to this problem. Here, we evaluate the performance of four approaches for estimating missing values in trait databases (K‐nearest neighbour (kNN), multivariate imputation by chained equations (mice), missForest and Phylopars), and test whether imputed datasets retain underlying allometric relationships among traits.

Starting with a nearly complete trait dataset on the mammalian order Carnivora (using four traits), we artificially removed values so that the percent of missing values ranged from 10% to 80%. Using the original values as a reference, we assessed imputation performance using normalized root mean squared error. We also evaluated whether including phylogenetic information improved imputation performance in kNN, mice, and missForest (it is a required input in Phylopars). Finally, we evaluated the extent to which the allometric relationship between two traits (body mass and longevity) was conserved for imputed datasets by looking at the difference (bias) between the slope of the original and the imputed datasets or datasets with missing values removed.

Three of the tested approaches (mice, missForest and Phylopars), resulted in qualitatively equivalent imputation performance, and all had significantly lower errors than kNN. Adding phylogenetic information into the imputation algorithms improved estimation of missing values for all tested traits. The allometric relationship between body mass and longevity was conserved when up to 60% of data were missing, either with or without phylogenetic information, depending on the approach. This relationship was less biased in imputed datasets compared to datasets with missing values removed, especially when more than 30% of values were missing.

Imputations provide valuable alternatives to removing missing observations in trait databases as they produce low errors and retain relationships among traits. Although we must continue to prioritize data collection on species traits, imputations can provide a valuable solution for conducting macroecological and evolutionary studies using life‐history trait databases.
Rescaled “Rebel Cities”, Nationalization, and the Bourgeois Utopia: Dialectics Between Urban Social Movements and Regulation for Japan's Homeless
Authors: Hayashi Mahito
Published: July 2014

Urban social movements (USMs) and regulation have co‐evolved in Japan to deal with homelessness, spatializaing their politics on the national and subnational scales. The author first theorizes these USM–regulation relationships as scale‐oriented dialectics between two opposing forces—“commoning and othering”—both of which in my view are always internalized in today's “rebel cities” (Harvey 2012,Rebel Cities, Verso). Then, he analyzes two trajectories of USMs that attempted commoning—ie radical opening up of public goods/spaces within “zones of weakness” (Lefebvre)—against policing and workfare disciplines. The author detects “rescaling” dialectics in the case of Yokohama and “nationalizing” dialectics in the case of Tokyo. Lastly, through exploring and refreshing Engels's notion of the (petit‐)bourgeois utopia, the author concludes that our commoning projects and imaginaries are constrained by capitalist urban form that spatially others the homeless; but truly revolutionary moments of commoning emerge whenever people—even temporarily—conquer the fetishism of the public/private binary embedded in this urban form.
Acta Ophthalmologica: History 1970–88
Authors: Norn Mogens
Published: July 2014

This is my personal memories concerning the Nordic periodical Acta Ophthalmologica in the period 1970–88. Poul Brændstrup was scientific secretary for Acta 1950–70 and chief editor 1970–75. His many important scientific works and enormous work for Acta is described, but also personal topics are mentioned. Acta meetings in the Danish Ophthalmol Society (DOS) and in the Nordic ophtalmol. Congresses are discussed. A referee‐system is established from 1976, but with political contra scientific motives. Only a few papers arrived to Acta. A catastrophe in 1978 is mentioned. The new secretary Ingelise Truberg did an enormous work for the next ten years. Erik Jørgensen (1928–90) was our printer, and from 1975 our idealistic publisher after Munksgaard. The economy became better and the number of papers of high quality increased. The relationship to the new Nordic periodical Oftalmolog was discussed in 1982.
Monocyte activation, brain‐derived neurotrophic factor (BDNF), and S100B in bipolar offspring: a follow‐up study from adolescence into adulthood
Authors: Mesman Esther , Hillegers Manon HJ , Ambree Oliver , Arolt Volker , Nolen Willem A , Drexhage Hemmo A
Published: July 2014

Objectives

There is increasing evidence that both immune and neurochemical alterations are involved in the pathogenesis of bipolar disorder; however, their precise role remains unclear. In this study, we aimed to evaluate neuro‐immune changes in a prospective study on children of patients with bipolar disorder.

Methods

Bipolar offspring, from the prospective Dutch bipolar offspring study (n = 140), were evaluated cross‐sectionally within a longitudinal context at adolescence, young adulthood, and adulthood. We examined the expression of 44 inflammation‐related genes in monocytes, the cytokines pentraxin 3 (PTX3), chemokine ligand 2 (CCL2), and interleukin‐1β (IL‐1β), and brain‐derived neurotrophic factor (BDNF) and S100 calcium binding protein B (S100B) in the serum of bipolar offspring and healthy controls.

Results

During adolescence, bipolar offspring showed increased inflammatory gene expression in monocytes, high serum PTX3 levels, but normal CCL2 levels. BDNF levels were decreased, while S100B levels were normal. During young adulthood, monocyte activation remained, although to a lesser degree. Serum PTX3 levels remained high, and signs of monocyte migration became apparent through increased CCL2 levels. BDNF and S100B levels were not measured. At adulthood, circulating monocytes had lost their activation state, but CCL2 levels remained increased. Both BDNF and S100B were now increased. Abnormalities were independent of psychopathology state at all stages.

Conclusions

This study suggests an aberrant neuro‐immune state in bipolar offspring, which followed a dynamic course from adolescence into adulthood and was present irrespective of lifetime or future mood disorders. We therefore assumed that the aberrant neuro‐immune state reflects a general state of vulnerability for mood disorders rather than being of direct predictive value.
Assessing reflective thinking in solving design problems: The development of a questionnaire
Authors: Hong Yi‐Chun , Choi Ikseon
Published: July 2014

Reflection is a critical factor in solving design problems. Using good methods to observe designers' reflection is essential to inform the design of the learning environments that support the development of design problem‐solving skills. In this study, we have developed and validated a novel self‐reporting questionnaire as an efficient instrument to explore reflection, called Assessing Reflective Thinking in Solving Design Problems (ARTiD). This questionnaire has been developed based on the three‐dimensional model for reflective thinking: the timing, the objects and the levels of reflection. A total of 294 undergraduate and graduate students in the fields of engineering, computer science and instructional design were recruited to participate in one of four iterative, formative tests through which reliability and validity analyses were performed to revise and confirm the questionnaire. Examples of participants' reflection patterns were demonstrated to show the practical value of this questionnaire. In conclusion, the final version of ARTiD was presented as a valid instrument to explore students' reflection for research and educational practice. In addition, we found that ARTiD can be used as an effective learning tool to guide student designers' reflections toward better learning and performance.
Digital simulation‐based training: A meta‐analysis
Authors: Gegenfurtner Andreas , Quesada‐Pallarès Carla , Knogler Maximilian
Published: July 2014

This study examines how design characteristics in digital simulation‐based learning environments moderate self‐efficacy and transfer of learning. Drawing on social cognitive theory and the cognitive theory of multimedia learning, the meta‐analysis psychometrically cumulated k = 15 studies of 25 years of research with a total sample size of N = 2274 learners. The findings indicate that high levels of user control result in higher estimates of self‐efficacy and transfer. Offering assessment feedback after rather than during training led to higher efficacy beliefs and transfer. Effects of social, narrative and multimedia characteristics were nonsignificant. Implications for computer‐based instructional design and directions for future research associated with motivational outcomes in technology‐enhanced learning are discussed.
Tricyclic and SSRI usage influences the association between BMI and health risk factors
Authors: Serodio K. J. , Ardern C. I. , Rotondi M. A. , Kuk J. L.
Published: July 2014

To determine if selective‐serotonin reuptake inhibitors (SSRIs) and tricyclic antidepressants (TCAs) influence the association between obesity and cardiovascular disease risk, participants from the Third National Health and Nutrition Examination Survey (NHANES III; 1988–1992) and continuous NHANES (1999–2009, n = 18 274) were used. For a given body mass index (BMI), individuals taking SSRIs (n = 219) tended to have significantly better health risk profiles with lower systolic blood pressure (P = 0.002) and higher high‐density lipoprotein (P = 0.003) compared with non‐users. Conversely, those who used TCAs (n = 116) had significantly worse health risk profiles with higher diastolic blood pressure (P ≤ 0.0001) and triglycerides (P = 0.023) as compared with non‐users for a given BMI. Insulin resistance (HOMA‐IR) was higher in TCA users and those with larger BMIs, whereby the differences in insulin resistance between TCA users and non‐users was greater with higher BMIs (interaction effect: P = 0.013). Furthermore, individuals taking SSRIs were less likely to have cardiovascular disease than non‐users (odds ratio, 95% confidence interval = 0.50, 0.33–0.75) for a given BMI, with no differences by TCA use (odds ratio = 0.74, 0.44–1.24). SSRI and TCA use may alter how body weight relates with cardiovascular risk. When prescribing antidepressant medications, it may be necessary to monitor and consider body weight and cardiovascular risk profile of individual patients.
Epicutaneous exposure to nickel induces nickel allergy in mice via a MyD88‐dependent and interleukin‐1‐dependent pathway
Authors: Vennegaard Marie T. , Dyring‐Andersen Beatrice , Skov Lone , Nielsen Morten M. , Schmidt Jonas D. , Bzorek Michael , Poulsen Steen S. , Thomsen Allan R. , Woetmann Anders , Thyssen Jacob P. , Johansen Jeanne D. , Ødum Niels , Menné Torkil , Geisler Carsten , Bonefeld Charlotte M.
Published: July 2014

Background

Several attempts to establish a model in mice that reflects nickel allergy in humans have been made. Most models use intradermal injection of nickel in combination with adjuvant to induce nickel allergy. However, such models poorly reflect induction of nickel allergy following long‐lasting epicutaneous exposure to nickel.

Objective

To develop a mouse model reflecting nickel allergy in humans induced by epicutaneous exposure to nickel, and to investigate the mechanisms involved in such allergic responses.

Methods

Mice were exposed to NiCl2 on the dorsal side of the ears. Inflammation was evaluated by the swelling and cell infiltration of the ears. T cell responses were determined as numbers of CD4+ and CD8+ T cells in the draining lymph nodes. Localization of nickel was examined by dimethylglyoxime staining.

Results

Epicutaneous exposure to nickel results in prolonged localization of nickel in the epidermis, and induces nickel allergy in mice. The allergic response to nickel following epicutaneous exposure is MyD88‐dependent and interleukin (IL)‐1 receptor‐dependent, but independent of toll‐like receptor (TLR)‐4.

Conclusion

This new model for nickel allergy that reflects epicutaneous exposure to nickel in humans shows that nickel allergy is dependent on MyD88 and IL‐1 receptor signalling, but independent of TLR4.
A systematic review of enhanced recovery care after colorectal surgery in elderly patients
Authors: Bagnall N. M. , Malietzis G. , Kennedy R. H. , Athanasiou T. , Faiz O. , Darzi A.
Published: July 2014

Aim

Enhanced recovery after surgery (ERAS) can decrease complications and reduces hospital stay. Less certain is whether elderly patients can fully adhere to and benefit from ERAS. We aimed to determine the safety, feasibility and efficacy of enhanced recovery after colorectal surgery in patients aged ≥ 65 years old.

Method

A systematic search of Medline, EMBASE and Cochrane was performed to identify (i) studies comparing elderly patients managed with ERAS vs traditional care, (ii) cohort studies of ERAS with results of elderly vs younger patients and (iii) any case series of ERAS in elderly patients. End‐points of interest were length of hospital stay, complications, mortality, readmission and re‐operation, and ERAS protocol adherence.

Results

Sixteen studies were included. Two randomized controlled trials demonstrated shorter hospital stay in elderly patients with ERAS compared with elderly patients with non‐ERAS (9 vs 13.2 days, P < 0.001; 5.5 vs 7 days, P < 0.0001). Fewer complications occurred with ERAS in both randomized controlled trials (27.4% vs 58.6%, P < 0.0001; 5% vs 21.1%, P = 0.045). The majority of observational studies did not show differences in outcome between elderly and younger patients in terms of hospital stay, morbidity or mortality. Inconsistent findings between cohort studies may reflect the disparities in ERAS protocol definitions or differences in study populations.

Conclusion

ERAS can be safely applied to elderly patients to reduce complications and shorten length of hospital stay. Further studies are required to assess whether elderly patients are able to adhere to, and benefit from, ERAS protocols to the same extent as younger patients.