bluuebunny/crossref_metadata_2025 huggingface dataset:
Graph-regularized dual Lasso for robust eQTL mapping
Authors: Cheng Wei , Zhang Xiang , Guo Zhishan , Shi Yu , Wang Wei
Published: June 2014

Motivation: As a promising tool for dissecting the genetic basis of complex traits, expression quantitative trait loci (eQTL) mapping has attracted increasing research interest. An important issue in eQTL mapping is how to effectively integrate networks representing interactions among genetic markers and genes. Recently, several Lasso-based methods have been proposed to leverage such network information. Despite their success, existing methods have three common limitations: (i) a preprocessing step is usually needed to cluster the networks; (ii) the incompleteness of the networks and the noise in them are not considered; (iii) other available information, such as location of genetic markers and pathway information are not integrated.

Results: To address the limitations of the existing methods, we propose Graph-regularized Dual Lasso (GDL), a robust approach for eQTL mapping. GDL integrates the correlation structures among genetic markers and traits simultaneously. It also takes into account the incompleteness of the networks and is robust to the noise. GDL utilizes graph-based regularizers to model the prior networks and does not require an explicit clustering step. Moreover, it enables further refinement of the partial and noisy networks. We further generalize GDL to incorporate the location of genetic makers and gene-pathway information. We perform extensive experimental evaluations using both simulated and real datasets. Experimental results demonstrate that the proposed methods can effectively integrate various available priori knowledge and significantly outperform the state-of-the-art eQTL mapping methods.

Availability: Software for both C++ version and Matlab version is available at http://www.cs.unc.edu/∼weicheng/.

Contact:  weiwang@cs.ucla.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Privacy preserving protocol for detecting genetic relatives using rare variants
Authors: Hormozdiari Farhad , Joo Jong Wha J , Wadia Akshay , Guan Feng , Ostrosky Rafail , Sahai Amit , Eskin Eleazar
Published: June 2014

Motivation: High-throughput sequencing technologies have impacted many areas of genetic research. One such area is the identification of relatives from genetic data. The standard approach for the identification of genetic relatives collects the genomic data of all individuals and stores it in a database. Then, each pair of individuals is compared to detect the set of genetic relatives, and the matched individuals are informed. The main drawback of this approach is the requirement of sharing your genetic data with a trusted third party to perform the relatedness test.

Results: In this work, we propose a secure protocol to detect the genetic relatives from sequencing data while not exposing any information about their genomes. We assume that individuals have access to their genome sequences but do not want to share their genomes with anyone else. Unlike previous approaches, our approach uses both common and rare variants which provide the ability to detect much more distant relationships securely. We use a simulated data generated from the 1000 genomes data and illustrate that we can easily detect up to fifth degree cousins which was not possible using the existing methods. We also show in the 1000 genomes data with cryptic relationships that our method can detect these individuals.

Availability: The software is freely available for download at http://genetics.cs.ucla.edu/crypto/.

Contact:  fhormoz@cs.ucla.edu or eeskin@cs.ucla.edu

Supplementary information:  Supplementary data are available at Bioinformatics online
LICRE: unsupervised feature correlation reduction for lipidomics
Authors: Wong Gerard , Chan Jeffrey , Kingwell Bronwyn A. , Leckie Christopher , Meikle Peter J.
Published: June 2014

Motivation: Recent advances in high-throughput lipid profiling by liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) have made it possible to quantify hundreds of individual molecular lipid species (e.g. fatty acyls, glycerolipids, glycerophospholipids, sphingolipids) in a single experimental run for hundreds of samples. This enables the lipidome of large cohorts of subjects to be profiled to identify lipid biomarkers significantly associated with disease risk, progression and treatment response. Clinically, these lipid biomarkers can be used to construct classification models for the purpose of disease screening or diagnosis. However, the inclusion of a large number of highly correlated biomarkers within a model may reduce classification performance, unnecessarily inflate associated costs of a diagnosis or a screen and reduce the feasibility of clinical translation. An unsupervised feature reduction approach can reduce feature redundancy in lipidomic biomarkers by limiting the number of highly correlated lipids while retaining informative features to achieve good classification performance for various clinical outcomes. Good predictive models based on a reduced number of biomarkers are also more cost effective and feasible from a clinical translation perspective.

Results: The application of LICRE to various lipidomic datasets in diabetes and cardiovascular disease demonstrated superior discrimination in terms of the area under the receiver operator characteristic curve while using fewer lipid markers when predicting various clinical outcomes.

Availability and implementation: The MATLAB implementation of LICRE is available from https://sites.google.com/site/licrerepository/

Contact:  gerard.wong@bakeridi.edu.au or gerard.wong@unimelb.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cloud4Psi: cloud computing for 3D protein structure similarity searching
Authors: Mrozek Dariusz , Małysiak-Mrozek Bożena , Kłapciński Artur
Published: June 2014

Summary: Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased computational resources that are not always available. Cloud computing provides huge amounts of computational power that can be provisioned on a pay-as-you-go basis. We have developed the cloud-based system that allows scaling of the similarity searching process vertically and horizontally. Cloud4Psi (Cloud for Protein Similarity) was tested in the Microsoft Azure cloud environment and provided good, almost linearly proportional acceleration when scaled out onto many computational units.

Availability and implementation: Cloud4Psi is available as Software as a Service for testing purposes at: http://cloud4psi.cloudapp.net/ . For source code and software availability, please visit the Cloud4Psi project home page at http://zti.polsl.pl/dmrozek/science/cloud4psi.htm .

Contact:  dariusz.mrozek@polsl.pl
The Scramble conversion tool
Authors: Bonfield James K.
Published: June 2014

Motivation: The reference CRAM file format implementation is in Java. We present ‘Scramble’: a new C implementation of SAM, BAM and CRAM file I/O.

Results: The C implementation of for CRAM is 1.5–1.7× slower than BAM at decoding but 1.8–2.6× faster at encoding. We see file size savings of 34–55%.

Availability and implementation: Source code is available at http://sourceforge.net/projects/staden/files/io_lib/ under the BSD software licence.

Contact:  jkb@sanger.ac.uk

Supplementary information : Supplementary data are available at Bioinformatics online.
Multiple populations in globular clusters and the origin of the Oosterhoff period groups
Authors: Jang Sohee , Lee Young-Wook , Joo Seok-Joo , Na Chongsam
Published: June 2014

The presence of multiple populations is now well established in most globular clusters in the Milky Way. In light of this, here we propose a new model to explain the origin of the Sandage period-shift and the difference in mean period of type ab RR Lyrae variables between the two Oosterhoff groups. In our model, the instability strip in the metal-poor group II clusters, such as M15, is populated by second-generation stars (G2) with enhanced helium and CNO abundances, while the RR Lyraes in the relatively metal-rich group I clusters such as M3 are produced mostly by first-generation stars (G1) without these enhancements. This population shift within the instability strip with metallicity can create the observed period-shift between the two groups, as both helium and CNO abundances play a role in increasing the period of RR Lyraes. The presence of more metal-rich clusters having Oosterhoff-intermediate characteristics, such as NGC 1851, as well as of most metal-rich clusters having RR Lyraes with the longest periods (group III) can also be reproduced, as more helium-rich third and later generations of stars (G3) penetrate into the instability strip with a further increase in metallicity. Therefore, although there are systems in which the suggested population shift cannot be a viable explanation, for the most general cases our models predict that the RR Lyraes are produced mostly by G1, G2 and G3 for the Oosterhoff groups I, II and III, respectively.
Coxsackievirus B3 regulates T-cell infiltration into the heart by lymphocyte function-associated antigen-1 activation via the cAMP/Rap1 axis
Authors: Shim Seung-Hyun , Kim Dae-Sun , Cho Whajung , Nam Jae-Hwan
Published: June 2014

Coxsackievirus B3 (CVB3) infection can trigger myocarditis and can ultimately lead to dilated cardiomyopathy. It is known that CVB3-induced T-cell infiltration into cardiac tissues is one of the pathological factors causing cardiomyocyte injury by inflammation. However, the underlying mechanism for this remains unclear. We investigated the mechanism of T-cell infiltration by two types of CVB3: the H3 WT strain and the YYFF attenuated strain. T-cell activation was confirmed by changes in the distribution of lymphocyte function-associated antigen-1 (LFA-1). Finally, we identified which viral gene was responsible for LFA-1 activation. CVB3 could infect and activate T-cellsin vivoandin vitro, and activated T-cells were detected in CVB3-infected mouse hearts. LFA-1 expressed on the surface of these T-cells had been activated through the cAMP/Rap1 pathway. Recombinant lentiviruses expressing VP2 of CVB3 could also induce LFA-1 activation via an increase in cAMP, whilst VP2 of YYFF did not. These results indicated that CVB3 infection increased cAMP levels and then activated Rap1 in T-cells. In particular, VP2, among the CVB3 proteins, might be critical for this activation. This VP2–cAMP–Rap1–LFA-1 axis could be a potential therapeutic target for treating CVB3-induced myocarditis.
Mitochondrial DNA variation and structure among North American populations ofMegaselia scalaris
Authors: Lesavoy Bret S. , McGaugh Suzanne E. , Noor Mohamed A. F.
Published: June 2014

The scuttle flyMegaselia scalarisis a pest species whose larvae consume living or dead plant or animal tissue, and parasitize humans. Although known to exist on most continents, often transported passively with humans, the connectivity between populations has not been investigated. We use mitochondrialcytochrome Bsequences to investigate structure among North American isolates of this species. Despite small sample sizes, we detected statistically significant structure among populations. This finding suggests that local measures may be effective in controlling this pest species.
Evaluation ofde novotranscriptome assemblies from RNA-Seq data
Authors: Li Bo , Fillmore Nathanael , Bai Yongsheng , Collins Mike , Thomson James A. , Stewart Ron , Dewey Colin N.
Published: June 2014

De novoRNA-Seq assembly facilitates the study of transcriptomes for species without sequenced genomes, but it is challenging to select the most accurate assembly in this context. To address this challenge, we developed a model-based score, RSEM-EVAL, for evaluating assemblies when the ground truth is unknown. Our experiments show that RSEM-EVAL correctly reflects assembly accuracy, as measured by REF-EVAL, a refined set of ground-truth-based scores that we also developed. With the guidance of RSEM-EVAL, we assembled the transcriptome of the regenerating axolotl limb; this assembly compares favorably to a previous assembly.
Coordination polymer chains built from CuIIand adipate ions linked by hydrogen bonds to form a three-dimensional framework structure
Authors: Setifi Zouaoui , Boutebdja Mehdi , Setifi Fatima , Merazig Hocine , Glidewell Christopher
Published: June 2014

In the title compound,catena-poly[bis[(2,2′-bipyridine-κ2N,N′)(1,1,3,3-tetracyano-2-ethoxypropenido-κN)copper(II)]-μ4-hexanedioato-κ6O1,O1′:O1:O6,O6′:O6], [Cu2(C9H5N4O)2(C6H8O4)(C10H8N2)2]n, the adipate (hexanedioate) dianion lies across a centre of inversion in the space groupP\overline{1}. The CuIIcentre adopts a distorted form of axially elongated (4+2) coordination, and the CuIIand adipate components form a one-dimensional coordination polymer from which the 2,2′-bipyridine and 1,1,3,3-tetracyano-2-ethoxypropenide components are pendent, and where each adipate dianion is bonded to four different CuIIcentres. The coordination polymer chains are linked into a three-dimensional framework structure by a combination of C—H...N and C—H...O hydrogen bonds, augmented by a π–π stacking interaction.
Value and store brand identification in food products
Authors: Rubio Natalia , Villaseñor Nieves , Oubiña Javier
Published: June 2014

Purpose

– Store brands have become consolidated in the food market and are currently considered real brands. The purpose of this paper is to determine the factors that contribute to consumers’ identification with store brands, as well as the possible effect of consumers’ identification with store brands on their loyalty to the retail establishment.

Design/methodology/approach

– The paper achieves its goal by reviewing the academic literature on the topic and proposing and validating a theoretical model for consumer-store brand identification. The theoretical model is validated through an empirical study of the Spanish market for food products using data gathered from individuals responsible for shopping for their homes who claim to have purchased store brand food products at least once. Structural equations modeling is then used to estimate and perform a multigroup analysis for heavy and light buyers of store brands.

Findings

– The results obtained reveal, first, that consumers’ store brand identification mediates the relationship between their value consciousness and their loyalty to the retail establishment that manages a broad, competitive portfolio of store brands. Second, the study demonstrates the effect of other variables, such as perceived risk associated with the purchase of store brands, their perceived value and consumer satisfaction. Finally, the results show important differences between heavy and light buyers of store brands.

Research limitations/implications

– The main limitations of this research derive from the factors conditioning the information. Store brand value was analyzed on an aggregate level, for the Spanish food products market. Future research should include other store brands (e.g. premium store brands), control for store brands with different labels and expand the area of application to new product categories and new countries.

Practical implications

– The results obtained have interesting implications for food retailers. These implications concern the management of value store brands in the product portfolio to achieve loyalty to the retail establishment among value-conscious consumers (who constitute the main target of value store brands).

Originality/value

– This paper analyzes consumer brand identification in an area that has not been studied to date: store brands. It contributes interesting and very useful findings for retailers who commercialize these brands in their establishments. The line of research on brand identification is quite new in academic research and has arisen due to the importance for companies of constructing close, lasting connections with the consumer.
Nutritional characteristics of mung bean foods
Authors: Kumar Dahiya Pradeep , Nout M.J.R. , A. van Boekel Martinus , Khetarpaul Neelam , Bala Grewal Raj , Linnemann Anita
Published: June 2014

Purpose

– The purpose of this paper is to address malnourishment in developing countries by a food-based approach in which locally produced and consumed foods are improved by applying food processing techniques that benefit the amount and availability of desirable nutrients.

Design/methodology/approach

– To facilitate this approach, this paper reports on the composition and in vitro micronutrient accessibility of 14 traditional mung bean foods from India in relation to their preparation methods.

Findings

– Proximate composition, in vitro mineral accessibility, phytic acid and polyphenol contents varied among the range of products. Products requiring either fermentation or germination, had higher in vitro iron, zinc and calcium accessibility. Average in vitro iron, zinc and calcium accessibility of the mung bean products were 16, 9 and 418 mg kg−1 dry weight. Phytic acid and polyphenols averaged 2.1 and 1.8 g kg−1 dry weight, respectively, and were negatively correlated with in vitro mineral accessibility.

Practical implications

– Different mung bean products (100 g) cover 12.0-59.5, 5.2-45.6, 4.2-28.6 and 1.1-7.1 per cent of the recommended dietary allowance for protein, iron, zinc and calcium, respectively, for seven- to nine-year-old Indian children.

Originality/value

– This study demonstrated the wide range of traditional mung bean foods in India and presents options to tackle malnourishment by a food-based approach.
Food and culture: in search of a Singapore cuisine
Authors: Catherine Henderson Joan
Published: June 2014

Purpose

– The purpose of this paper is to illuminate aspects of the relationship between food and culture with particular emphasis on globalisation and its consequences, the ways in which food can represent people and places, and interest if food heritage. Issues are discussed within the context of Singapore.

Design/methodology/approach

– A case study methodology is employed using published information from assorted sources, both online and in conventional print form, supplemented by personal observation.

Findings

– A country's food culture is found to be influenced by globalising forces, yet these do not always overwhelm local distinctions and the international and domestic can co-exist and coalesce. Food is also shown to be a critical dimension of ethnic and national identity and to have a heritage worthy of protection. In addition, it is a tourist attraction which affords insights into destination culture. Defining a national cuisine, however, is complicated in multiracial societies and origins and ownership of so-called national dishes may be disputed.

Practical implications

– Enhanced knowledge about the wider role of food in established and emerging Asian economies and societies can improve understanding of its significance for residents and tourists, helping in formulating strategies to meet needs.

Originality/value

– New insights are offered into the meanings of food in relatively young countries of mixed races and how cuisines evolve and interact.
The implementation of an environmental management system in the not-for-profit sector
Authors: R.T. White Gareth , Lomax Matthew , Parry Glenn
Published: June 2014

Purpose

– This paper aims to examine the implementation of the Eco-Management and Audit Scheme (EMAS) in a non-profit, small-to-medium sized-enterprise (SME) in the UK.

Design/methodology/approach

– A four-year participatory action research study is made upon knowledge transfer partnerships between the University of the West of England and the Royal Bath and West Society.

Findings

– Through the adoption of EMAS, the organisation was able to identify operational improvements as well as make significant efforts to improve its environmental performance, reducing its carbon footprint by 30 tCO2e per annum and gaining new business.

Research limitations/implications

– The study is made upon a single not-for-profit organisation in the UK.

Practical implications

– It presents the costs, benefits and challenges that the organisation faced. Techniques that were used to successfully manage the environmental management systems (EMS) development are also discussed. The investigation identifies deficiencies in the materials that are provided to support companies that are seeking EMAS certification. To improve the uptake of these EMS and assist companies in their successful pursuit of ISO 14001 and EMAS, this supporting documentation requires enhancement.

Originality/value

– There has been relatively little empirical research around the development and benefits of organisational EMS. Even less has focussed upon the specific constraints and opportunities that face non-profit organisations when implementing EMAS. This paper addresses this gap, identifying its costs and tangible benefits.
IFRS and convergence in China and the USA
Authors: Moser Randy
Published: June 2014

Purpose

– The purpose of this paper is to perform a brief examination of International Financial Reporting Standards (IFRS) and the progress towards IFRS convergence in the accounting environments of China and the USA, providing useful information on the current status and future of IFRS convergence in these countries.

Design/methodology/approach

– A range of IFRS-related literature from 1993 to 2013 was analyzed to provide the current status of IFRS and to determine the past, present and future of IFRS convergence in the country examinations.

Findings

– IFRS convergence and adoption has occurred on a global scale due to the call for a single set of standards. China's most significant obstacles include training accounting professionals and becoming more involved in the International Accounting Standards Board (IASB) standard setting process. The USA's most significant obstacle is completing the Securities and Exchange Commission roadmap milestones, which will progressively move the accounting industry towards IFRS convergence.

Research limitations/implications

– These findings have been limited to an overview of IFRS convergence and adoption within China and the USA. Additional research opportunities exist by examining how successful countries have been in protecting individual economic interests by working with the IASB in the standard setting process for the IFRS, as opposed to being passive in the process. One economic indicator that should be examined is foreign direct investment, which has major impacts on country development and can be influenced by financial standards such as IFRS.

Practical implications

– China and the USA both have milestones identified in this paper that will need to be reached before benefits may be reaped from the converging to IFRS.

Originality/value

– These findings show that IFRS standards are being implemented globally in many nations, providing a common set of reporting tools to businesses and investors. Through these standards, China and the USA are working to be even more competitive forces in financial markets.
Internal multiple attenuation by Kirchhoff extrapolation
Authors: Lipari Vincenzo , Fortini Carlo , Spadavecchia Emmanuel , Bienati Nicola
Published: June 2014

Surface‐related multiple elimination is the leading methodology for surface multiple removal. This data‐driven approach can be extended to interbed multiple prediction at the expense of a huge increase of the computational burden. This cost makes model‐driven methods still attractive, especially for the three dimensional case. In this paper we present a methodology that extends Kirchhoff wavefield extrapolation to interbed multiple prediction. In Kirchhoff wavefield extrapolation for surface multiple prediction a single round trip to an interpreted reflector is added to the recorded data. Here we show that interbed multiples generated between two interpreted reflectors can be predicted by applying the Kirchhoff wavefield extrapolation operator twice. In the first extrapolation step Kirchhoff wavefield extrapolation propagates the data backward in time to simulate a round trip to the shallower reflector. In the second extrapolation step Kirchhoff wavefield extrapolation propagates the data forward in time to simulate a round trip to the deeper reflector. In the Kirchhoff extrapolation kernel we use asymptotic Green's functions. The prediction of multiples via Kirchhoff wavefield extrapolation is possibly sped up by computing the required traveltimes via a shifted hyperbola approximation. The effectiveness of the method is demonstrated by results on both synthetic and field data sets.
Relationship between growth and standard metabolic rate: measurement artefacts and implications for habitat use and life‐history adaptation in salmonids
Authors: Rosenfeld Jordan , Van Leeuwen Travis , Richards Jeffrey , Allen David
Published: June 2014

Mass‐specific standard metabolic rate (SMR, or maintenance metabolism) varies greatly among individuals. Metabolism is particularly sensitive to variation in food consumption and growth creating the potential for significant bias in measured SMR for animals that are growing (e.g. juveniles) or of uncertain nutritional status.

Consequently, interpreting individual variation in metabolism requires a sound understanding of the potentially confounding role of growth and the relative importance of fixed (genetic) vs. environmental drivers of SMR variation.

We review the role of growth in measured SMR variation in juvenile salmonids, with the goals of (i) understanding the contribution of growth (and food consumption) to SMR variation through ontogeny, (ii) understanding the relative contributions of tissue maintenance and biosynthesis (overhead costs of growth) to apparent SMR variation, and (iii) using intrinsic growth effects on SMR to model how alternate life‐history strategies may influence growth and measured SMR in juvenile salmonids.

SMR measures on juveniles, even when post‐absorptive, may be inflated by delayed growth‐associated overhead costs, unless juveniles are on a maintenance ration (i.e. not growing). Empirical measurements of apparent SMR in food restricted vs. satiated 2–5 g juvenile salmon demonstrate that estimates may be inflated by as much as 67% due to delayed overhead costs of growth, even when SMR measurements are taken 35 h post‐feeding.

These results indicate that a substantial component of variation in apparent SMR among juvenile salmonids may be associated with (i) environmentally driven variation in ration (where elevated SMR measurements are an artefact of delayed growth overhead costs), (ii) intrinsic (genetic) or plastic organ‐system trade‐offs related to increasing investment in metabolically expensive digestive tissue responsible for processing food and (iii) intrinsic (genetic) variation in maximum body size and growth among individuals or life‐history types. We suggest that selection for differences in adult body size among resident and anadromous forms leading to differences in juvenile growth trajectories may contribute to both SMR variation and habitat segregation in freshwater, where juveniles with higher growth are constrained to foraging in high velocity habitats to meet their greater consumption needs.
Prehospital management of supraventricular tachycardia in Victoria, Australia: Epidemiology and effectiveness of therapies
Authors: Smith Gavin , McD Taylor David , Morgans Amee , Cameron Peter
Published: June 2014

Objective

The present study examined patient demographics, characteristics and the effectiveness of current prehospital supraventricular tachycardia (SVT) management by ambulance paramedics in Victoria, Australia.

Method

We conducted a retrospective study of all Victorian patients attended by paramedics between 14 February 2012 and 13 February 2013, where SVT was the initial or final diagnosis. Patients were excluded if SVT was not captured on ECG, incomplete data were recorded, or SVT began after initial assessment. Data were extracted from the VACIS® clinical data warehouse. Accuracy of paramedic SVT diagnosis was examined.

Results

Nine hundred and thirty‐three patients were enrolled, including 882 (94.5%) adults and 564 (60.5%) women. Mean adult and paediatric (<18 years) patient ages were 57.5 (SD 18.1) and 10.0 (SD 4.5) years, respectively. Median ambulance response time was 11.0 (IQR 8.0) min. Paramedics correctly identified SVT in 119/123 (96.7%, 95% CI: 91.5, 99.0) of adult ECG strips examined. There were 273/882 (31.0%) patients who spontaneously reverted while in paramedic care. Valsalva manoeuvre was undertaken by 212/882 (24.0%) patients and reverted the SVT in 99/358 (27.7%) attempts. Verapamil was administered to 38/882 (4.3%) patients and reverted 33 (86.8%). Aramine was administered to 43/882 (4.9%) patients and 35 reverted following administration (81.4%). Synchronised cardioversion (70 J) reverted four patients at first attempt. Ultimately, 438 (49.7%) patients remained in SVT on arrival at hospital.

Conclusion

Patient characteristics associated with SVT are more likely to be middle‐aged women with a history of hypertension and hypercholesterolaemia. Therapies were underutilised leading to reduced clinical guideline effectiveness. Where therapies were instigated, reversion rates are greater than previously reported.
Mild traumatic brain injury in children: Management practices in the acute care setting
Authors: Kool Bridget , King Vivienne , Chelimo Carol , Dalziel Stuart , Shepherd Michael , Neutze Jocelyn , Chambers Nikki , Wells Susan
Published: June 2014

Objective

Accurate diagnosis, treatment and follow up of children suffering mild traumatic brain injury (MTBI) is important as post‐concussive symptoms and long‐term disability might occur. This research explored the decisions clinicians make in their assessment and management of children with MTBI in acute care settings, and identified barriers and enablers to the delivery of best‐practice care.

Methods

A purposeful sample of 29 clinicians employed in two metropolitan paediatric EDs and one Urgent Care clinic was surveyed using a vignette‐based questionnaire that also included domains of guideline awareness, attitudes to MTBI care, use of clinical decision support systems, and knowledge and skills for practising evidence‐based healthcare.

Results

Overall, the evaluation and management of children presenting acutely with MTBI generally followed best‐practice guidelines, particularly in relation to identifying intracranial injuries that might require surgical intervention, observation for potential deterioration, adequate pain management and the provision of written head injury advice on discharge. Larger variation emerged in regard to follow‐up care and referral pathways. Potential barriers to best‐ practice were lack of guideline awareness, attitudes to MTBI, and lack of time or other priorities.

Conclusions

Opportunities exist to improve care for children who present in acute care settings following mild traumatic brain injury. These include having up‐to‐date guidelines that are consistent across acute care settings; providing clearer pathways for referral and follow up; targeting continuing medical education towards potential complications; and providing computerised decision support so that assessment and management are conducted systematically.
Including community composition in biodiversity–productivity models
Authors: Sandau Nadine , Rohr Rudolf P. , Naisbit Russell E. , Fabian Yvonne , Bruggisser Odile T. , Kehrli Patrik , Aebi Alexandre , Bersier Louis‐Félix
Published: June 2014

Studies on biodiversity and ecosystem functioning (BEF) have elicited debate over the interpretation of the positive relationship between species richness and plant productivity. Manipulating richness cannot be achieved without affecting composition; it is thus essential to consider the latter in statistical models.

We firstly review existing approaches that use species richness as an explanatory variable and propose modifications to improve their performance. We use an original data set to illustrate the analyses. The classical method where composition is coded as a factor with a level for each different species mixture can be improved by defining the levels using clustering. Methods based on ordinations reduce the dimensionality of plant composition and use the new coordinates as fixed effects; they provide a much better fit to our observations.

Secondly, we develop a new method where composition is included as a similarity matrix affecting the residual variance–covariance. Similarity in composition between plots is treated in the same way as shared evolutionary history between species in phylogenetic regression. We find that it outperforms the other models.

We discuss the different approaches and suggest that our method is particularly suited for observational studies or for manipulative studies where plant diversity is not kept constant by weeding. By treating species composition in an intuitive and sensible way, it offers a valuable and powerful complement to existing models.
Socioeconomic evaluation of well‐characterized allergy to staple foods in adults
Authors: Jansson S.‐A. , Protudjer J. L. P. , Arnlind Heibert M. , Bengtsson U. , Kallström‐Bengtsson I. , Marklund B. , Middelveld R. J. M. , Rentzos G. , Sundqvist A. C. , Åkerström J. , Östblom E. , Dahlén S.‐E. , Ahlstedt S.
Published: June 2014

Background

The aim of the present study was to evaluate if total, direct, indirect, and intangible costs differ between a cohort of adults with well‐characterized allergy to staple foods (‘cases’) and controls.

Methods

Swedish adults with objectively diagnosed food allergy to cow′s milk, hen′s egg, and/or wheat were recruited at an outpatient allergy clinic. Controls age‐ and sex‐matched to cases were recruited from the same geographic area. For assessing the household costs of food allergy, a disease‐specific socioeconomic questionnaire, developed within EuroPrevall, was utilized.

Results

Overall annual total costs at the household level were significantly higher among adults with food allergy compared with controls (the difference amounted to 8164 €), whereas direct costs did not differ between cases and controls. However, household healthcare costs and costs for medicines were significantly higher for cases vs controls. Furthermore, indirect costs were significantly higher for households with food‐allergic adults vs households without food‐allergic adults. Specifically, more time was spent on performing domestic tasks due to a family member's food‐allergy‐related illness, as well as shopping and preparing food, and seeking food‐allergy‐related information. Presence of food allergy also affected intangible costs. Adults with food allergy experienced overall lower health status compared with controls.

Conclusions

Swedish adults with allergy to staple foods have higher total costs determined as direct, indirect, and intangible costs using the disease‐specific socioeconomic questionnaire. Thus, total costs were 8164 € higher per year in households with at least one adult allergic to staple foods compared with controls.
CCL2 release by airway smooth muscle is increased in asthma and promotes fibrocyte migration
Authors: Singh S. R. , Sutcliffe A. , Kaur D. , Gupta S. , Desai D. , Saunders R. , Brightling C. E.
Published: June 2014

Background

Asthma is characterized by variable airflow obstruction, airway inflammation, airway hyper‐responsiveness and airway remodelling. Airway smooth muscle (ASM) hyperplasia is a feature of airway remodelling and contributes to bronchial wall thickening. We sought to investigate the expression levels of chemokines in primary cultures of ASM cells from asthmatics vs healthy controls and to assess whether differentially expressed chemokines (i) promote fibrocyte (FC) migration towards ASM and (ii) are increased in blood from subjects with asthma and in sputum samples from those asthmatics with bronchial wall thickening.

Methods

Chemokine concentrations released by primary ASM were measured by MesoScale Discovery platform. The chemokine most highly expressed by ASM from asthmatics compared with healthy controls was confirmed by ELISA, and expression of its cognate chemokine receptor by FCs was examined by immunofluorescence and flow cytometry. The role of this chemokine in FC migration towards ASM was investigated by chemotaxis assays.

Results

Chemokine (C‐C motif) ligand 2 (CCL2) levels were increased in primary ASM supernatants from asthmatics compared with healthy controls. CCR2 was expressed on FCs. Fibrocytes migrated towards recombinant CCL2 and ASM supernatants. These effects were inhibited by CCL2 neutralization. CCL2 levels were increased in blood from asthmatics compared with healthy controls, and sputum CCL2 was increased in asthmatics with bronchial wall thickening.

Conclusions

Airway smooth muscle‐derived CCL2 mediates FC migration and potentially contributes to the development of ASM hyperplasia in asthma.
Supplementation of standard pre‐oxygenation with nasal prong oxygen or machine oxygen flush during a simulated leak scenario
Authors: Russell T. , Ng L. , Nathan E. , Debenham E.
Published: June 2014

The presence of a facemask leak significantly reduces the effectiveness of pre‐oxygenation and increases the risk of post‐induction hypoxia. We randomly assigned 24 healthy volunteers to a six‐period crossover trial with and without a simulated facemask leak. Pre‐oxygenation was performed using a standard anaesthesia machine circuit supplemented either by nasal prong oxygen or by anaesthesia machine flush oxygen. Each intervention was completed with both 3‐min tidal breathing and 8 deep breath techniques: end‐tidal oxygen fraction was used as the measure of pre‐oxygenation effectiveness. The presence of a stimulated mask leak significantly reduced the effectiveness of pre‐oxygenation regardless of the breathing method used. With a simulated facemask leak introduced, the mean (SD) end‐tidal oxygen fraction with the 3‐min tidal breath technique was 74.7 (9.3)% compared with 57.5 (6.2%) for the 8 deep breath technique with 3‐min tidal breathing and a leak. End‐tidal oxygen fractions increased by 11.0% (95% CI 7.8–14.3%) (p < 0.0001) with the addition of nasal prong oxygenation and 16.8% (13.6–20.0%) (p < 0.0001) with machine oxygen flush compared with standard pre‐oxygenation. When a leak is present, 3‐min tidal breathing with either nasal prong or anaesthesia machine flush oxygenation is an effective pre‐oxygenation method, and preferable to the 8 deep breath method.
Periocular sebaceous gland carcinoma: do androgen receptor (NR3C4) and nuclear survivin (BIRC5) have a prognostic significance?
Authors: Mulay Kaustubh , Shah Sneha J. , Aggarwal Ekta , White Valerie A. , Honavar Santosh G.
Published: June 2014

Purpose

The study aimed at evaluating the expression of androgen receptor (AR) and nuclear survivin (NS) in periocular sebaceous gland carcinoma (SGC) and to determine whether this expression is associated with histopathological features, markers of apoptosis and proliferation and with clinical outcomes.

Methods

This was a retrospective, comparative case series which included 56 patients with a biopsy‐proven periocular SGC. Immunohistochemical staining for AR, survivin, p53 and Ki‐67 was analysed in all cases.

Results

All patients expressed AR, p53 and Ki‐67 in the nucleus of tumour cells. Twenty‐four patients (42.8%) had a high AR score, and 32 patients (57.2%) had a low AR score. Twenty‐four (42.8%) patients expressed survivin in the nucleus of tumour cells. Nine (37.5%) had a high NS score, and 15 (62.5%) had a low NS score. Patients with a high AR score had a greater recurrence (p < 0.005), higher expression of Ki‐67 (p < 0.0001) and a lower p53 expression (p < 0.005). Nuclear expression of survivin correlated with a high Ki‐67 labelling index (0.0001) and low p53 expression (<0.005). Neither nuclear expression of survivin nor the NS score correlated with any clinicopathological features.

Conclusion

Expression of AR significantly impacts prognosis and is thus promising prognostic marker in periocular SGC.
Gender differences in biometry prediction error and intra‐ocular lens power calculation formula
Authors: Behndig Anders , Montan Per , Lundström Mats , Zetterström Charlotta , Kugelberg Maria
Published: June 2014

Purpose

To analyze changes over time in biometry prediction error (BPE) after cataract surgery with special reference to the impact of gender and the intra‐ocular lens (IOL) calculation formula.

Methods

About 65% of Swedish cataract surgery units participating in the outcome registration of the National Cataract Register (NCR) were included in this prospective register study. Data for planned and postoperative refraction and keratometry during the month of March 2004–2013 were analyzed, divided by gender. The newly introduced variables axial length and IOL calculation formula were analyzed for March 2013. Gender differences in BPE with correct sign (BPESign) and absolute biometry prediction error (BPEAbs) were compared for the Haigis' and Sanders‐Retzlaff‐Kraff T (SRK/T) formulas.

Results

The BPEAbs decreased throughout the study period. In 2004–2006, the BPEAbs was larger in women than in men (p < 0.05), but this difference disappeared from 2007. For 2004 through 2009, the mean BPESign was −0.105 ± 0.79D for women, but −0.003 ± 0.73D for men. After 2009, this myopic error for women gradually diminished. The Haigis' formula performed better in women than the SRK/T formula (p < 0.001); the SRK/T formula rendered a BPESign similar to that from 2004 to 2009 in women. Women had steeper corneas and shorter axial lengths than men (p < 0.001).

Conclusion

The myopic BPE in women – associated with steeper corneas and shorter axial lengths – is decreasing, possibly owing to an increased use of the Haigis' formula. Using the Haigis' formula to a higher extent can potentially further reduce the BPEs after cataract surgery.
The Influence of Improvements in Accounting Standards on Earnings Management: The Case of IFRS
Authors: Navarro‐García Juan Carlos , Madrid‐Guijarro Antonia
Published: June 2014

This article examines the effect of improvements in the quality of International Financial Reporting Standards (IFRS) on the level of earnings management. In order to achieve this aim, we study the accounting quality of German listed companies through discretionary accruals yielded from 1998 to 2006. We assess the effectiveness of efforts by the International Accounting Standards Board to improve IFRS by using two indices that consider the revision process of the standards, and their mandatory application. Our results indicate that the improvement of accounting standards quality significantly reduces the level of reported negative discretionary accruals of the German listed firms during the period of analysis, once incentive variables are controlled. Further, companies gradually assume the quality of the new standards from the moment they can be voluntarily applied.
Comprehending Comprehensive Income
Authors: Hodgson Allan , Russell Mark
Published: June 2014

Comprehensive income (CI) contains a mixture of realised, unrealised, temporary, persistent and recyclable elements. How, when and where these elements should be reported in income and equity have been issues intensively debated (and changed) by international regulators over the last 20 years. This article traces the major threads of the debate and places changes within the context of empirical academic research. Our contention is that the recent IAS 1 (AASB 101) Presentation of Financial Statements, effective 1 July 2012, has benefited from past academic research that focused on the value relevance from disaggregation and presentation of unrealised other comprehensive income (OCI). We conclude by outlining the equity posting and recycling to profit or loss (P&L) issues and assert that, because of the inconsistent nature and complexity of OCI, it would benefit from further research.
First report of exocrine epithelial glands in oestroid flies: the tachinid sexual patches (Diptera: Oestroidea: Tachinidae)
Authors: Cerretti Pierfilippo , Di Giulio Andrea , Romani Roberto , Inclan Diego J. , Whitmore Daniel , Di Giovanni Filippo , Scalici Massimiliano , Minelli Alessandro
Published: June 2014

Sexual patches are abdominal areas identifiable by modified setation, present in the males of several groups of Tachinidae (Diptera). We comparatively studied more than 40 species belonging to 24 genera representative of subfamilies known to bear these organs, using light microscopy and scanning (SEM) and transmission (TEM) electron microscopy. We provide a detailed characterization of the fine structure of the setae and microtrichia composing these sexual patches and of the underlying epithelium. Study of abdominal sections showed that, close to the patch area, the epidermis forms a thick layer composed of numerous secretory units of strictly associated cells, ending at the level of cuticular pores at the base of the setae. We hypothesize a secretory function of these structures. The segmental pattern of the sexual patches across the Tachinidae is defined and predictable. We note that almost all the segmental patterns share the presence of sexual patches on abdominal tergite 4, underscoring the diversity of male sexual specializations that occur on the fourth abdominal segment of muscomorph flies.
Soluble CD40-ligand (sCD40L, sCD154) plays an immunosuppressive role via regulatory T cell expansion in HIV infection
Authors: Jenabian M-A , Patel M , Kema I , Vyboh K , Kanagaratham C , Radzioch D , Thébault P , Lapointe R , Gilmore N , Ancuta P , Tremblay C , Routy J-P
Published: June 2014

CD40/CD40-ligand (CD40L) signalling is a key stimulatory pathway which triggers the tryptophan (Trp) catabolizing enzyme IDO in dendritic cells and is immunosuppressive in cancer. We reported IDO-induced Trp catabolism results in a T helper type 17 (Th17)/regulatory T cell (Treg) imbalance, and favours microbial translocation in HIV chronic infection. Here we assessed the link between sCD40L, Tregs and IDO activity in HIV-infected patients with different clinical outcomes. Plasmatic sCD40L and inflammatory cytokines were assessed in anti-retroviral therapy (ART)-naive, ART-successfully treated (ST), elite controllers (EC) and healthy subjects (HS). Plasma levels of Trp and its metabolite Kynurenine (Kyn) were measured by isotope dilution tandem mass spectrometry and sCD14 was assessed by enzyme-linked immunosorbent assay (ELISA). IDO-mRNA expression was quantified by reverse transcription–polymerase chain reaction (RT–PCR). The in-vitro functional assay of sCD40L on Treg induction and T cell activation were assessed on peripheral blood mononuclear cells (PBMCs) from HS. sCD40L levels in ART-naive subjects were significantly higher compared to ST and HS, whereas EC showed only a minor increase. In ART-naive alone, sCD40L was correlated with T cell activation, IDO-mRNA expression and CD4 T cell depletion but not with viral load. sCD40L was correlated positively with IDO enzymatic activity (Kyn/Trp ratio), Treg frequency, plasma sCD14 and inflammatory soluble factors in all HIV-infected patients. In-vitro functional sCD40L stimulation induced Treg expansion and favoured Treg differentiation by reducing central memory and increasing terminal effector Treg proportion. sCD40L also increased T cell activation measured by co-expression of CD38/human leucocyte antigen D-related (HLA-DR). These results indicate that elevated sCD40L induces immunosuppression in HIV infection by mediating IDO-induced Trp catabolism and Treg expansion.