bluuebunny/crossref_metadata_2025 huggingface dataset:
Consensus assessment of the contamination level of publicly available cyanobacterial genomes
Authors: Cornet Luc , Meunier Loïc , Van Vlierberghe Mick , Léonard Raphaël R. , Durieu Benoit , Lara Yannick , Misztak Agnieszka , Sirjacobs Damien , Javaux Emmanuelle J. , Philippe Hervé , Wilmotte Annick , Baurain Denis
Published: April 2018

BACKGROUND

Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes.

RESULTS

As reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods).

CONCLUSIONS

Our results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases.
Long non-coding RNAs in wild wheat progenitors
Authors: Pieri Alice , Enrico Pè Mario , Bertolini Edoardo
Published: April 2018

Triticum urartuandAegilops tauschiiare the diploid progenitors of the hexaploidTriticum aestivum(AuAuBBDD), donors of the Auand D genome respectively. In this work we investigate the long noncoding RNAs (lncRNAs) component of the genomes of these two wild wheat relatives. Sixty-eight RNA-seq libraries generated from several organs and conditions were retrieved from public databases. We annotated and characterized 14,515T. urartuand 20,908Ae. tauschii bona-fidelncRNA transcripts that show features similar to those of other plant and animal counterparts. Thousands of lncRNAs were found significantly modulated in different organs and exhibited organ specific expression, with a predominant accumulation in the spike, fostering the hypothesis of their crucial role in reproductive organs. Most of the organ-specific lncRNAs were found associated with transposable elements (TEs), indicating the possible role of TEs in lncRNA origin, differentiation and function. The majority ofT. urartuandAe. tauschiilncRNAs appear to be species-specific; nevertheless, we found some lncRNAs conserved between the two wheat progenitors, highlighting the presence and conservation of exonic splicing enhancers sites in multi-exon conserved lncRNAs. In addition, we found cases of lncRNA conservation and theircisregulatory regions spanning the wheat pre-domestication and post-domestication period. Altogether, these results represent the first comprehensive genome-wide encyclopedia of lncRNAs in wild wheat relatives, and they provide clues as to the hidden regulatory pathway mediated by long noncoding RNAs in these largely unexplored wheat progenitors.
A kinetic model for fluorescence microscopy experiments in disordered media that contains binding sites and obstacles
Authors: Shkilev V.P.
Published: April 2018

A model is proposed that describes the diffusion of molecules in a disordered medium with binding sites (traps) and obstacles (barriers). The equations of the model are obtained using the subordination method. As the parent process, random walks on a disordered lattice are taken, described by the random barriers model. As the leading process, the renewal process that corresponds to the multiple-trapping model is taken. Theoretical expressions are derived for the curves obtained in experiments using fluorescence microscopy (FRAP, FCS and SPT). Generalizations of the model are proposed, allowing to take into account correlations in the mutual arrangement of traps and barriers. The model can be used to find parameters characterizing the diffusion and binding properties of biomolecules in living cells.
Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding
Authors: Franklin Meghan Whitney , Slusky Joanna S.G.
Published: April 2018

I.

As a structural class, tight turns can control molecular recognition, enzymatic activity, and nucleation of folding. They have been extensively characterized in soluble proteins but have not been characterized in outer membrane proteins (OMPs), where they also support critical functions. We clustered the 4-6 residue tight turns of 110 OMPs to characterize the phi/psi angles, sequence, and hydrogen bonding of these structures. We find significant differences between reports of soluble protein tight turns and OMP tight turns. Since OMP strands are less twisted than soluble strands they favor different turn structures types. Moreover, the membrane localization of OMPs yields different sequence hallmarks for their tight turns relative to soluble protein turns. We also characterize the differences in phi/psi angles, sequence, and hydrogen bonding between OMP extracellular loops and OMP periplasmic turns. As previously noted, the extracellular loops tend to be much longer than the periplasmic turns. We find that this difference in length is due to the broader distribution of lengths of the extracellular loops not a large difference in the median length. Extracellular loops also tend to have more charged residues as predicted by the charge-out rule. Finally, in all OMP tight turns, hydrogen bonding between the sidechain and backbone two to four residues away plays an important role. These bonds preferentially use an Asp, Asn, Ser or Thr residue in a beta or pro phi/psi conformation. We anticipate that this study will be applicable to future design and structure prediction of OMPs.
ACDtool: a web-server extending the original Audic-Claverie statistical test to the comparison of large data sets of counts
Authors: Claverie Jean-Michel , Thi Ngan TA
Published: April 2018

Motivation

More than 20 years ago, our laboratory published an original statistical test (referred to as the Audic-Claverie (AC) test in the literature) to identify differentially expressed genes from the pairwise comparison of counts of cognate RNA-seq reads (then called “expressed sequence tags”) determined in different conditions. Despite its antiquity and the publications of more sophisticated software packages, this original article continued to gather more than 200 citations per year, indicating the persistent usefulness of the simple AC test for the community. This prompted us to propose a fully revamped version of the AC test with a user interface adapted to the diverse and much larger datasets produced by contemporary omics techniques.

Results

We implemented ACDtool as an interactive, freely accessible web service proposing 3 types of analyses: 1) the pairwise comparison of individual counts, 2) pairwise comparisons of arbitrary large lists of counts, 3) the all-at-once pairwise comparisons of multiple datasets. Statistical computations are implemented using standard R functions and mathematically reformulated as to accommodate all practical ranges of count values. ACDtool can thus analyze datasets from transcriptomic, proteomic, metagenomics, barcoding, ChlP'seq, population genetics, etc, using the same mathematical approach. ACDtool is particularly well suited for comparisons of large datasets without replicates.

Availability

ACDtool is at URL: www.igs.cnrs-mrs.fr/acdtool/

Contact

Jean-Michel.Claverie@univ-amu.fr

Supplementary information

none.
Impact of Brownian moment and thermophoresis on magnetohydrodynamic flow of magnetic nanofluid past an elongated sheet in the presence of thermal diffusion
Authors: Sulochana C. , Ashwinkumar G.P.
Published: April 2018

Purpose

The purpose of this paper is to report the impact of thermophoresis and Brownian moment on MHD two-dimensional forced convection flow of nanofluid past a permeable stretching sheet in the presence of thermal diffusion.

Design/methodology/approach

The flow governing PDEs are reduced to ODEs by utilizing pertinent transmutations and then resolved by employing a fourth-order Runge-Kutta-based shooting technique. The energy and diffusion equations are incorporated with Brownian motion, thermophoresis and Soret parameters. The velocity, thermal and concentration attributes along with skin friction factor, local Nusselt and Sherwood number are discussed under the influence of sundry pertinent parameters and presented with the assistance of graphical and tabular values.

Findings

The results infer that Sherwood number is accelerated by Soret parameter but it controls the thermal transport rate. And also, Brownian and thermophoresis play a vital role in enhancing heat conduction process.

Originality/value

Considering the industrial applications of flow of magnetic nanofluid over a stretching surface, this paper presents the solution of the flow problem considering thermophoresis, Brownian motion, magnetic field and thermal diffusion effects. In addition, the aim and objectives of this paper fills a gap in the industry.
On the development of a predictive functional trait approach for studying terrestrial arthropods
Authors: Brousseau Pierre‐Marc , Gravel Dominique , Handa Ira Tanya
Published: April 2018

The characterization of ecological communities with functional traits allows to consider simultaneously the ability of a species to survive and reproduce in an environment, its interactions with other species and its effects on the ecosystem.

Functional traits have been studied mainly by plant ecologists, but are increasingly common in the study of other taxa including arthropods. Arthropods represent a group for which a functional trait approach could be highly profitable because of their high diversity, abundance, ubiquity and role in many important ecological processes.

This review synthesizes two decades of functional trait research on terrestrial arthropods. We show that while the approach has gained popularity, particularly in the last decade, the absence of clearly postulated hypotheses is a recurrent problem limiting generalization. Furthermore, studied traits are often poorly related to studied functions. To address these problems, we propose a step‐by‐step protocol to postulate clear hypotheses prior to trait selection and emphasize the need for a common set of more generalizable traits in future studies.

Extending the functional trait approach to arthropods opens the door to improving our understanding of interspecific interactions and potential links between response and effect traits. We present the concept of trait‐matching with several examples of arthropod traits known to be effective predictors of consumer–resource interactions.

The development of a successful functional trait approach for terrestrial arthropods will necessitate an understanding of relevant traits, standardized measurement protocols and open access databases to share this information. Such progress will provide ecologists with a new set of tools to answer broad questions in several fields including the study of community assembly, ecological networks and multitrophic functionality.
Urban land expansion in Indonesia 1992–2012: evidence from satellite‐detected luminosity
Authors: Olivia Susan , Boe‐Gibson Geua , Stitchbury Glen , Brabyn Lars , Gibson John
Published: April 2018

Land conversion to urban use typically accompanies economic development but raises concerns about food security. Debates of these issues often rely on incomplete and incompatible evidence. This study uses satellite‐detected luminosity, from 1992 to 2012, to examine the urban land expansion of 41 major urban areas in Indonesia. The trend annual expansion rate is 2.0 per cent, which is comparable to the rate for India and just one‐third of the rate for China, as estimated with the same data and methods. Prior to the Asian Financial Crisis in 1997/98, the rate of urban expansion was faster, and the income elasticity of urban expansion was much higher. About 85 per cent of the area of urban expansion had formerly been grassland, shrub or woodland, and just 7.0 per cent was former cropland so food security concerns about urban expansion may be overstated.
Scaling Up Community Action for Tackling Climate Change
Authors: Shaw Deirdre , Cumbers Andrew , McMaster Robert , Crossan John
Published: April 2018

Tackling climate change requires a set of deeply intertwined geographical responsibilities whereby actors at and across different geographical scales are intimately connected. Creating effective strategies requires far more than an invocation for individual behavioural change in thinking globally and acting locally, but attention to the multi‐scalar conflicts, tensions and also opportunities to develop the most appropriate collective responses. In this paper, we use the example of community gardening initiatives in a large UK city to critically interrogate the problems facing groups at the local neighbourhood level in pursuing sustainability agendas. We focus on the organizational imperative to create a multi‐scalar food policy partnership at the city level as a way of confronting dominant global neoliberal urban competitiveness agendas. Our results emphasize the critical importance of scalar politics in enabling effective climate change strategies.
Reimagining the Scales, Dimensions and Fields of Socio‐ecological Sustainability
Authors: O'Reilly Dermot , Allen Stephen , Reedy Patrick
Published: April 2018

This paper critiques the two‐dimensional (hierarchical–spatial) focus on scales evident in management and organizational studies, and the capitalist ecological modernization (CEM) paradigm that dominates current corporate and governmental approaches to sustainability. Our contribution is to propose a more complex and nuanced understanding of scale, which incorporates social, political, temporal and material dimensions. We propose a heuristic framework from Harvey, in order to evaluate different paradigms of socio‐ecological organizing: specifically, the dominant paradigm of CEM against a social ecology (SE) alternative. We explore the divergent conceptions of, and relative importance placed upon, concepts of scale, grain, level and field in these two contrasting paradigms. Our analysis highlights the limitations and contradictions of the CEM expression of scale, namely its predominant focus on measurement and expansion through ‘economies of scale’. By offering an alternative conception of the links between scales, grains, levels and social fields, we show how this enriches the conceptualization of potential forms of socio‐ecological organizing and opens up the potential for alternative modes of organizing socio‐ecological sustainability.
Scaling as an Organizational Method: Ethnographic Explorations of Two Danish Sustainability Organizations
Authors: Papazu Irina , Nelund Mette
Published: April 2018

Organization studies have shown limited interest in the part that scaling plays in organizational responses to climate change and sustainability. Moreover, while scales are viewed as central to the diagnosis of the organizational challenges posed by climate change and sustainability, the role of scaling in meeting these challenges has not yet been recognized. By analysing two ethnographic case studies, conducted at Samsø Energy Academy and Farendløse Cider Works, respectively, the authors identify scaling as a core activity of the sustainability organization. The two organizations studied each situate their operations at the heart of the climate change problematic – one in organic farming, the other in renewable energy – and, employing what the authors term ‘the method of scaling’, they impose order on the world in which they operate. The method of scaling helps the organizations relate their actions to the ambiguous concepts of sustainability and climate change. The authors find that the two organizations’ scaling activities occur in three modes: rejection, innovation and conscious adoption of core concepts such as sustainability and climate change. These modes of scaling help organizations turn something as immense as the climate into a small and manageable problem, thus making abstract concepts part of concrete, organizational practice.
Dash for Gas: Climate Change, Hegemony and the Scalar Politics of Fracking in the UK
Authors: Nyberg Daniel , Wright Christopher , Kirk Jacqueline
Published: April 2018

This paper investigates the political contestation over hydraulic fracturing of shale gas, or ‘fracking’, in the UK. Based on an analysis of four public inquiries, it shows how both proponents and opponents of fracking employed scaling to mobilize interests by connecting (or disconnecting) fracking to spatial and temporal scales. The analysis explains how a fossil fuel hegemony was reproduced by linking local and specific benefits to nationally or globally recognized interests such as employment, energy security and emission reductions. The paper contributes to recent debates on environmental political contestation by showing how scaling enables the linkage of competing interests by alternating between spatial (e.g. local vs. global) and temporal (e.g. short term vs. long term) horizons. The authors argue that scaling allows dominant actors to uphold contradictory positions on climate change, which contributes to explaining the current disastrous political climate impasse.
Sustainability: Issues of Scale, Care and Consumption
Authors: Chatzidakis Andreas , Shaw Deirdre
Published: April 2018

This paper investigates how consumers interested in sustainability are affected by conflicts in caring and scale. Contrasting previous emphasis relating scale to production, the paper illustrates how scale influences consumption and social reproduction, including consumers’ more concrete preoccupations with caring about and for themselves, significant others and, not least, the planet. The paper makes three contributions to the nascent management literature in this field. First, it illustrates how scalar logics at urban through to global levels influence seemingly micro‐social routine consumption decisions. Second, it develops an approach that emphasizes the scale‐sensitivity of consumer decision‐making around sustainability and the conflicts inherent in caring. Third, it addresses critiques of current studies preoccupied with processes of production rather than social reproduction and illustrates the critical role that consumption plays in the social construction of scales. Based on these findings, we argue that policy promoting sustainability may be misplaced in that it does not sufficiently acknowledge how people's consumption and caring decisions are nested in relational and spatial contexts.
Scaling Sustainability: Regulation and Resilience in Managerial Responses to Climate Change
Authors: Goworek Helen , Land Chris , Burt George , Zundel Mike , Saren Mike , Parker Martin , Lambe Brendan
Published: April 2018

This paper introduces the special issue of the British Journal of Management on ‘Scaling Sustainability: Regulation and Resilience in Managerial Responses to Climate Change’, providing an overview of the key issues in scaling sustainability, comprising an analysis of the six papers in the special issue. We discuss the complex relationship between micro, meso and macro scales, in the context of organizations’, managers’ and consumers’ complicity in the creation and intensification of climate‐changing conditions. In networking multiple sites into a ‘global’ scale, managers and organizations can lose sight of the situated, localized nature of the position from which they perform the global. We conclude that a key factor in the capacity and speed at which local actions can be scaled up is the connection of sustainability‐related activities by intermediary organizations that can generate resonance between multiple sites through association or alliance, rather than imposing a single logic. Thus, more resilient approaches, which acknowledge the significance of the interconnection between scales, are required to effectively scale sustainability strategies upwards or downwards.
Insurance and Climate Change Risk Management: Rescaling to Look Beyond the Horizon
Authors: Thistlethwaite Jason , Wood Michael O.
Published: April 2018

Climate change represents a significant financial risk to the insurance industry, but research has yet to assess whether the industry is managing this risk. Through the application of scale as a vertically nested hierarchy of relationships, this paper seeks to evaluate whether insurers are ‘rescaling’ risk management practices to accommodate the temporal and spatial uncertainty associated with climate change. This framework is applied to a content analysis of 178 (183) firm responses to the 2012 (2015) U.S. National Association of Insurance Commissioners Climate Risk Disclosure Survey to detect evidence of rescaling through climate change risk management (CCRM). The results reveal that the majority of companies do not integrate climate change into their risk management practices, but reinsurers are rescaling in a greater proportion than primary insurers. This finding confirms that a nested spatial and temporal scale in the insurance industry creates resistance to CCRM. The use of scale contributes to emerging scholarship on organizations and climate change by offering a framework for measuring organizational responses and justifying a research agenda on rescaling strategies as a means of risk management.
Administrative Agencies and the Collaborative Game: An Analysis of the Influence of Government Agencies in Collaborative Policy Implementation
Authors: Vento Isak , Sjöblom Stefan
Published: April 2018

Over the past decades, most countries have witnessed an increase in collaborative arrangements for engaging stakeholders in collective decision‐making processes. Despite the fact that the role of the state in the collaborative structures has been one of the highly debated issues, there is still a need for a more comprehensive understanding of how governmental agencies affect the performance of collaborative actions. This article develops a framework for systematic analyses of collaborative effects on policy performance. Using PROCESS OLS regression, the authors apply the framework to project‐level Cohesion Policy implementation in Finland – that is, to collaborative arrangements embedded in a rather fragmented and complex administrative context. The typical state characteristics of a Nordic country make Finland an interesting case for studying the interaction in collaborative arrangements between the administration and external agencies in a modern welfare state. The results presented in this article show that government agencies have a considerable moderating impact on the relationships between collaborative qualities and performance. The impact is, however, dependent on the responsiveness of the external agent to the bureaucratic rationale. The results underline the importance of more holistic approaches for analyzing complex collaborative constellations, focusing particularly on interaction effects between potential explanatory factors.
An exploration into how the impact of interventions for pupils with special educational needs can be sustainable and support long term progress
Authors: Belli Clare
Published: April 2018

This short piece of action research seeks to identify the characteristics which ensure that the impact from external interventions delivered by Southampton Advisory Outreach Service for SEND can be sustained over time. It considers how the service can work with schools to establish self‐sustaining systems which reduce dependency, thereby freeing the service to focus resources where there is greatest need. The research suggests that sustainable progress depends on the continued setting of specific targets which allow progress to be measured and evidenced over time. It also suggests, however, that schools need to consider the wider progress made by pupils, which cannot be captured by narrow progress measures. Furthermore, the research identifies some key factors which ensure pupils continue to make progress once external support is withdrawn. These include consistency in how support is delivered, and effective communication systems that help to maintain consistent approaches to support and allow for adaptation as part of the cycle of ‘assess, plan, do and review’. The article also considers how schools retain motivation to continue with recommendations once external support is withdrawn and the conditions that are needed to foster ongoing commitment.
Teachers and students with severe learning difficulties working together to co‐construct personal narratives using Storysharing®: the teacher perspective
Authors: Bunning Karen , Muggeridge Rebecca , Voke Katie
Published: April 2018

The telling of personal stories is a feature of everyday life. Young people with learning difficulties may find it difficult to report what has happened to them. A project was set up to investigate the impact of Storysharing® on the co‐construction of personal narratives by staff and students in a special school. The current study investigated the teacher's perspective. The sample was comprised of four special education teachers who had been involved in the implementation of Storysharing®. Semi‐structured interviews were carried out at the end of the intervention period. The data were analysed using thematic analysis. Three organising themes emerged from the data: ‘Enactment Process’; ‘Benefits to Child’; and ‘Curriculum.’ The Storysharing® intervention appeared to be positively associated with perceived changes to the educational practice of the teachers, revealing its potential for developing narrative in the classroom.
Teacher Preparedness in the use of Co‐teaching in Inclusive Classrooms
Authors: Chitiyo Jonathan , Brinda Wayne
Published: April 2018

Co‐teaching is a widely used instructional approach to meet the needs of all students in inclusive classrooms across the globe. Despite the widespread implementation of the practice, little is known about how teachers are prepared to use it. This study examined the extent to which 77 teachers were prepared to use co‐teaching. Results indicated that a majority of the teachers are underprepared in its use. Recommendations and implications are discussed.
Why ‘science for all’ is only an aspiration: staff views of science for learners with Special Educational Needs and Disabilities
Authors: Essex Jane
Published: April 2018

Teacher and support staff perceptions of science learning, and specifically engagement with science outreach, by pupils with Special Educational Needs and Disabilities (SEND) were ascertained through questionnaires. The responses indicated that science is seen as serving distinctive learning purposes when undertaken by learners with SEND. Staff who accompanied SEND pupils to science outreach events expressed more positive views about separate outreach events for SEND pupils than other respondents, in line with current policy expectations of differentiated classroom practice. The desire for different provision for SEND learners also appeared to be associated with the staffs’ pastoral concerns about their pupils and their reluctance to let their pupils ‘fail’. The data suggests that, despite policy and legislative reform in the UK, curriculum science is still viewed primarily as a means to career progression for an able minority, rather than as an educational and cultural entitlement for all.
Making a Difference: Dyslexia and Social Identity in Educational Contexts
Authors: Caskey Jacqueline , Innes Peter , Lovell Geoff P.
Published: April 2018

Dyslexia is known as a Learning Disability (LD), a reading disability and a neurological disability; yet there is confusion about dyslexia and the associated support required in learning. Challenges are experienced by adult students with dyslexia in both social and organisational contexts. This study explored the life experiences of adult students with dyslexia, in Technical and Further Education (TAFE) Colleges in Australia. The shift from a prior negative self‐perception to a current positive social identity in adult students with dyslexia can be developed through key supporting relationships and interactions in educational institutions.
On Ek and Jak In Middle Norwegian: Mixed Methods In Historical Sociolinguistics
Authors: Blaxter Tam , Kinn Kari
Published: April 2018

Work in historical sociolinguistics can broadly be divided into quantitative work which examines population‐level trends in past language use, and qualitative work which documents and explains the usage of individuals or within particular texts. In this paper, we argue for an approach which combines both of these. Using mixed methods we can achieve all the advantages of both qualitative and quantitative approaches, revealing the complexity of language use in real social contexts but situating it in a well‐described view of the historical processes at play. We demonstrate our approach with an exploration of the rise of ‘broken’ forms of the first person singular nominative pronoun in the history of Norwegian. We chart the overall progression and social patterning of the change using kernel density estimation, regression and geographically weighted regression. We then explore the wealth of fascinating local and ephemeral patterns by examining usage of particular individuals and texts.
Seeing Like a City‐State: Behavioural Planning and Governance in Egypt's First Affordable Gated Community
Authors: Simcik Arese Nicholas
Published: April 2018

Haram City is Egypt's first ‘affordable’ gated community, hosting both aspirational middle‐class homeowners and resettled poor urban residents. Amidst legal ambiguity during Egypt's 2011–2013 revolutionary period, the management team of this public–private partnership was tasked with creating a ‘fully self‐sufficient’ city. While Haram City is the product of top‐down ‘seeing like a state’ master planning (Scott, ), the day‐to‐day resolution of class vulnerabilities and disputes over ‘reasonableness’ in city life requires forms of interpersonal adjudication otherwise addressed through local urban law—‘seeing like a city’ (Valverde, ). This article uses ethnography of management techniques aiming to ‘upgrade behaviour’ to theorize that a private entity, in a strategically indeterminate relationship with the state, reconciles future‐oriented planning and storied prejudices by merging two visions of governance. Imitating the repertoire of urban law, managers plan the very realm of bottom‐up decision making. They then adapt top‐down urban planning to bottom‐up dispute resolution to spatially consolidate the ‘consensual’ outcomes of a rigged game. Evoking both colonial Egyptian vagrancy laws and neoliberal paternalist welfare, ‘seeing like a city‐state’ governance amounts to authoritarianism that conceals itself within custom, appearing neutral so as to plan streets, codes and inner lives at once.
Safety and harm in school: promoting the perspectives of students with intellectual disability
Authors: Robinson Sally
Published: April 2018

Violence and abuse towards schools students with intellectual disability is a pervasive and long‐standing problem. In recent research conducted with students with intellectual disability, their families and education providers about safety and harm in school, a concerning discord emerged between the nature of harms described by students and their families and the systemic responses available for redress. To explore this resistant space, this paper draws on a human‐rights framework for young people's participation (Lundy, 2007, British Educational Research Journal, 33, 927). Applying the framework to the study findings highlights a number of areas in which the participation of children and young people with disability sheds new light on long‐standing problems, including the role of safe spaces, student voice, adult audiences and increasing the influence of students’ perspectives on policy and practice. These findings are significant for policy and practice to better recognise the structural barriers in place which make it both more likely that students with disability will experience harm and that they will find it more difficult to bring this to light; and to align systems responses with the lived experience of students, families and individual educators so that harm can be quickly redressed and expectations raised for a safe and happy school life.
Rapporteur‐shadow rapporteur networks in the European Parliament: The strength of small numbers
Authors: HÄGE FRANK M. , RINGE NILS
Published: April 2018

Specialisation and delegation of policy leadership within committees is the norm rather than the exception in legislatures around the world. Yet, little research has studied the sub‐groups of lawmakers who serve as policy leaders on particular bills. This article uses conceptual and methodological tools from social network analysis to investigate the groups’ composition and relational structure. It tests the proposition that limited human resources lead lawmakers from small parties to more frequently engage with a greater number of colleagues from other parties across a wider range of policy areas. This may have important relational benefits that have the potential to outweigh the structural disadvantages of small party size. The article examines whether small party lawmakers participate more, are more central and have greater potential for brokerage in policy‐making networks, or if the constraints associated with small party size and/or particular ideological leanings prevent their realisation. Empirically, the analyses focus on working relationships between rapporteurs and shadow rapporteurs in the adoption of reports by standing committees of the 7th European Parliament, 2009–2014. Methodologically, a mixed methods approach is employed. The quantitative analyses show that small party size does not affect legislators’ participation in policy‐making networks, but that it increases legislators’ centrality and brokerage potential. Regarding ideology, being committed to democratic participation as a good in itself has a positive association with all three outcomes, while attitudes to European integration show no effect. The qualitative data suggest that the relational benefits of belonging to a small party partially mitigate the structural disadvantages associated with it. They also indicate that policy making in the European Parliament is quite inclusive, as any systematic exclusion tends to be the result of self‐marginalisation.
Can the online crowd match real expert judgments? How task complexity and coder location affect the validity of crowd‐coded data
Authors: HORN ALEXANDER
Published: April 2018

Crowd‐coding is a novel technique that allows for fast, affordable and reproducible online categorisation of large numbers of statements. It combines judgements by multiple, paid, non‐expert coders to avoid miscoding(s). It has been argued that crowd‐coding could replace expert judgements, using the coding of political texts as an example in which both strategies produce similar results. Since crowd‐coding yields the potential to extend the replication standard to data production and to ‘scale’ coding schemes based on a modest number of carefully devised test questions and answers, it is important that its possibilities and limitations are better understood. While previous results for low complexity coding tasks are encouraging, this study assesses whether and under what conditions simple and complex coding tasks can be outsourced to the crowd without sacrificing content validity in return for scalability. The simple task is to decide whether a party statement counts as positive reference to a concept – in this case: equality. The complex task is to distinguish between five concepts of equality. To account for the crowd‐coder's contextual knowledge, the IP restrictions are varied. The basis for comparisons is 1,404 party statements, coded by experts and the crowd (resulting in 30,000 online judgements). Comparisons of the expert‐crowd match at the level of statements and party manifestos show that the results are substantively similar even for the complex task, suggesting that complex category schemes can be scaled via crowd‐coding. The match is only slightly higher when IP restrictions are used as an approximation of coder expertise.
Review article: Investigations and the pregnant woman in the emergency department – part 1: Laboratory investigations
Authors: Morton Adam , Teasdale Stephanie
Published: April 2018

Accurate assessment of the pregnant patient in the ED depends on knowledge of physiological changes in pregnancy, and how these changes may impact on pathology tests, appearance on point‐of‐care ultrasound and electrocardiography. In addition the emergency physician needs to be cognisant of disorders that are unique to or more common in pregnancy. Part 1 of this review addresses potential deviations in laboratory investigation reference intervals resulting from physiological alterations in pregnancy, and the important causes of abnormal laboratory results in pregnancy. Part 2 will address the role of point‐of‐care ultrasound in pregnancy, physiological changes that may affect interpretation of point‐of‐care ultrasound, physiological changes in electrocardiography, and the safety of radiological procedures in the pregnant patient.
Efficacy of 7‐benzyloxyindole and other halogenated indoles to inhibit Candida albicans biofilm and hyphal formation
Authors: Manoharan Ranjith Kumar , Lee Jin‐Hyung , Lee Jintae
Published: April 2018

Certain pathogenic bacteria and yeast form biofilms on biotic and abiotic surfaces including medical devices and implants. Hence, the development of antibiofilm coating materials becomes relevant. The virulence of those colonizing pathogens can be reduced by inhibiting biofilm formation rather than killing pathogens using excessive amounts of antimicrobials, which is touted as one of the main reasons for the development of drug resistance. Candida albicans is an opportunistic fungal pathogen, and the transition of yeast cells to hyphal cells is believed to be a crucial virulence factor. Previous studies have shown that indole and its derivatives possess antivirulence properties against various bacterial pathogens. In this study, we used various indole derivatives to investigate biofilm‐inhibiting activity against C. albicans. Our study revealed that 7‐benzyloxyindole, 4‐fluoroindole and 5‐iodoindole effectively inhibited biofilm formation compared to the antifungal agent fluconazole. Particularly, 7‐benzyloxyindole at 0.02 mM (4.5 μg ml−1) significantly reduced C. albicans biofilm formation, but had no effect on planktonic cells, and this finding was confirmed by a 2,3‐bis‐(2‐methoxy‐4‐nitro‐5‐sulfophenyl)‐2H‐tetrazolium‐5‐carboxanilide (XTT) assay and three‐dimensional confocal laser scanning microscopy. Scanning electron microscopy analyses revealed that 7‐benzyloxyindole effectively inhibited hyphal formation, which explains biofilm inhibition. Transcriptomic analysis showed that 7‐benzyloxyindole downregulated the expressions of several hypha/biofilm‐related genes (ALS3, ECE1, HWP1 and RBT1). A C. albicans‐infected Caenorhabditis elegans model system was used to confirm the antivirulence efficacy of 7‐benzyloxyindole.
Exploring Nontraditional Participation as an Approach to Make Water Quality Trading Markets More Effective
Authors: Heberling Matthew T. , Thurston Hale W. , Nietch Christopher T.
Published: April 2018

Water quality trading (WQT) has the potential to be a low‐cost means for achieving water quality goals.WQTallows regulated wastewater treatment plants (WWTPs) facing discharge limits the flexibility to either reduce their own discharge or purchase pollution control from otherWWTPs or nonpoint sources (NPSs) such as agricultural producers. Under this limited scope, programs withNPSs have been largely unsuccessful at meeting water quality goals. The decision to participate in trading depends on many factors including the pollution control costs, uncertainty in pollution control, and discharge limits. Current research that focuses on makingWQTwork tends to identify how to increase participation by traditional traders such asWWTPs and agricultural producers. As an alternative, but complementary approach, we consider whether augmentingWQTmarkets with nontraditional participants would help increase the number of trades. Determining the economic incentives for these potential participants requires the development of novel benefit functions requiring not only economic considerations but also accounting for ecological and engineering processes. Existing literature on nontraditional participants in environmental markets tends to center on air quality and only increasing citizen participation as buyers. Here, we consider the issues for broadening participation (both buyers and sellers) inWQTand outline a multidisciplinary approach to begin evaluating feasibility.
Better performance of four‐dimension computed tomography as a localization procedure in normocalcemic primary hyperparathyroidism
Authors: Cunha‐Bezerra Phelipe , Vieira Ricardo , Amaral Fernando , Cartaxo Henrique , Lima Túlio , Montarroyos Ulisses , Bandeira Francisco
Published: April 2018

Introduction

The multi‐phase or four‐dimensional computed tomography (4D CT) has emerged as a promising technique for preoperative localization of parathyroid lesions in patients with primary hyperparathyroidism (PHPT), but little is known about its accuracy in patients with normocalcemic primary hyperparathyroidism (NPHPT).

Methods

A total of 18 patients diagnosed with PHPT underwent three methods of preoperative localization (4D CT, TC‐99‐Sestamibi scintigraphy and ultrasonography). After surgery, the results of imaging were compared with operative findings, pathological and biochemical data to evaluate the sensitivity and of each localization procedure.

Results

In NPHPT the sensitivity for identifying the parathyroid lesion, according to presentation of PHPT (hypercalcemic or normocalcemic), was better with 4DCT in comparison to USG and scintigraphy. In these patients, the sensitivity for lateralization was as follows: USG: 22% (95% CI 0–44.9), scintigraphy: 11.1% (95% CI 0–31.6), 4DCT: 55.6% (95% CI 23.1–88). In hypercalcemic patients the results were as follows: USG: 58.3% (95% CI 30.4–86.2), scintigraphy: 75% (95% CI 50.5–99.5), 4DCT: 75% (95% CI 50.5–99.5). There was a poor agreement between the three procedures in the identification of the parathyroid lesions, with Kappa coeficients of 0.292 and 0.01 for scintigraphy and 4DCT, respectively, in comparison to USG.

Conclusion

Our data showed that 4DCT had a better performance as a preoperative localization procedure of the parathyroid lesion in patients with NPHPT.
Determination of a suitable low‐dose abdominopelvic CT protocol using model‐based iterative reconstruction through cadaveric study
Authors: Moloney Fiachra , Twomey Maria , Fama Daniel , Balta Joy Y , James Karl , Kavanagh Richard G , Moore Niamh , Murphy Mary Jane , O'Mahony Siobhan M , Maher Michael M , Cryan John F , O'Connor Owen J
Published: April 2018

Introduction

Cadaveric studies provide a means of safely assessing new technologies and optimizing scanning prior to clinical validation. Reducing radiation exposure in a clinical setting can entail incremental dose reductions to avoid missing important clinical findings. The use of cadavers allows assessment of the impact of more substantial dose reductions on image quality. Our aim was to identify a suitable low‐dose abdominopelvic CT protocol for subsequent clinical validation.

Methods

Five human cadavers were scanned at one conventional dose and three low‐dose settings. All scans were reconstructed using three different reconstruction algorithms: filtered back projection (FBP), hybrid iterative reconstruction (60% FBP and 40% adaptive statistical iterative reconstruction (ASIR40)), and model‐based iterative reconstruction (MBIR). Two readers rated the image quality both quantitatively and qualitatively.

Results

Model‐based iterative reconstruction images had significantly better objective image noise and higher qualitative scores compared with both FBP and ASIR40 images at all dose levels. The greatest absolute noise reduction, between MBIR and FBP, of 34.3 HU (equating to a 68% reduction) was at the lowest dose level. MBIR reduced image noise and improved image quality even in CT images acquired with a mean radiation dose reduction of 62% compared with conventional dose studies reconstructed with ASIR40, with lower levels of objective image noise, superior diagnostic acceptability and contrast resolution, and comparable subjective image noise and streak artefact scores.

Conclusion

This cadaveric study demonstrates that MBIR reduces image noise and improves image quality in abdominopelvic CT images acquired with dose reductions of up to 62%.
Effects of geranylgeranylacetone upon cardiovascular diseases
Authors: Zeng Shengqiang , Wang Hong , Chen Zaihua , Cao Qianqiang , Hu Lin , Wu Yanqing
Published: April 2018

Heat shock proteins (HSPs) are an important family of protective proteins. They are involved actively in an array of cellular processes, including protective effects on the cardiovascular system in response to various stimuli. Increasing evidence shows that pharmacologic interventions that induce expression of HSPs may be a novel approach for the treatment of cardiovascular diseases. However, agents that induce expression of HSPs used previously are toxic or have harmful side effects, which limit their clinical application. Geranylgeranylacetone (GGA) is not only a widely used antiulcer agent in Asia, but also a nontoxic inducer of HSPs expression. It increases the expression of HSPs rapidly in the presence of ischemia, anoxia, oxidative stress, and toxicants, thereby having significant protective effects. The cardioprotective effects of GGA have been corroborated by experiments in vivo and in vitro. Importantly, several derivatives of GGA have been synthesized that have improved pharmaco‐chemical and HSPs‐boosting properties. In this review, the current knowledge and potential cardioprotective mechanisms of GGA are summarized comprehensively. We discuss the protective effects of GGA in cardiovascular diseases and myocardial injury induced by physical or chemical injury. Currently available information suggests that GGA could be employed as a novel pharmacologic intervention against cardiovascular disease.
After the Paris Agreement: What Role for the BRICS in Global Climate Governance?
Authors: Downie Christian , Williams Marc
Published: April 2018

The rising power of the BRICS is now at the centre of debates about the future of global governance. Despite the consensus that the political, economic and strategic differences between the BRICS trump the commonalities, the BRICS have managed a level of cooperation that has exceeded expectations. This has led to inquiries about their influence on several policy domains, especially global finance. However, less attention has been given to the role of the BRICS in global climate governance, especially in the aftermath of the Paris climate agreement in 2015. Following the Paris Agreement, and the US' withdrawal, this paper examines the capacity of the BRICS to re‐shape global climate governance. Based on an analysis of the emissions profile of the BRICS, and multilateral and bilateral meetings between BRICS countries since 2015, it argues that while significant obstacles to the BRICS acting as a coalition remain, there are areas that can be identified where cooperation could be scaled up in coming years.