bluuebunny/crossref_metadata_2025 huggingface dataset:
Architects in neural circuit design: Glia control neuron numbers and connectivity
Authors: Corty Megan M. , Freeman Marc R.
Published: November 2013

Glia serve many important functions in the mature nervous system. In addition, these diverse cells have emerged as essential participants in nearly all aspects of neural development. Improved techniques to study neurons in the absence of glia, and to visualize and manipulate glia in vivo, have greatly expanded our knowledge of glial biology and neuron–glia interactions during development. Exciting studies in the last decade have begun to identify the cellular and molecular mechanisms by which glia exert control over neuronal circuit formation. Recent findings illustrate the importance of glial cells in shaping the nervous system by controlling the number and connectivity of neurons.
Membrane domain organization of myelinated axons requires βII spectrin
Authors: Zhang Chuansheng , Susuki Keiichiro , Zollinger Daniel R. , Dupree Jeffrey L. , Rasband Matthew N.
Published: November 2013

The precise and remarkable subdivision of myelinated axons into molecularly and functionally distinct membrane domains depends on axoglial junctions that function as barriers. However, the molecular basis of these barriers remains poorly understood. Here, we report that genetic ablation and loss of axonal βII spectrin eradicated the paranodal barrier that normally separates juxtaparanodal K+ channel protein complexes located beneath the myelin sheath from Na+ channels located at nodes of Ranvier. Surprisingly, the K+ channels and their associated proteins redistributed into paranodes where they colocalized with intact Caspr-labeled axoglial junctions. Furthermore, electron microscopic analysis of the junctions showed intact paranodal septate-like junctions. Thus, the paranodal spectrin-based submembranous cytoskeleton comprises the paranodal barriers required for myelinated axon domain organization.
Parallel content-based sub-image retrieval using hierarchical searching
Authors: Yang Lin , Qi Xin , Xing Fuyong , Kurc Tahsin , Saltz Joel , Foran David J.
Published: November 2013

Motivation: The capacity to systematically search through large image collections and ensembles and detect regions exhibiting similar morphological characteristics is central to pathology diagnosis. Unfortunately, the primary methods used to search digitized, whole-slide histopathology specimens are slow and prone to inter- and intra-observer variability. The central objective of this research was to design, develop, and evaluate a content-based image retrieval system to assist doctors for quick and reliable content-based comparative search of similar prostate image patches.

Method: Given a representative image patch (sub-image), the algorithm will return a ranked ensemble of image patches throughout the entire whole-slide histology section which exhibits the most similar morphologic characteristics. This is accomplished by first performing hierarchical searching based on a newly developed hierarchical annular histogram (HAH). The set of candidates is then further refined in the second stage of processing by computing a color histogram from eight equally divided segments within each square annular bin defined in the original HAH. A demand-driven master-worker parallelization approach is employed to speed up the searching procedure. Using this strategy, the query patch is broadcasted to all worker processes. Each worker process is dynamically assigned an image by the master process to search for and return a ranked list of similar patches in the image.

Results: The algorithm was tested using digitized hematoxylin and eosin (H&E) stained prostate cancer specimens. We have achieved an excellent image retrieval performance. The recall rate within the first 40 rank retrieved image patches is ∼90%.

Availability and implementation: Both the testing data and source code can be downloaded from http://pleiad.umdnj.edu/CBII/Bioinformatics/.

Contact: lin.yang@uky.edu
SBML and CellML translation in Antimony and JSim
Authors: Smith Lucian P. , Butterworth Erik , Bassingthwaighte James B. , Sauro Herbert M.
Published: November 2013

Motivation: The creation and exchange of biologically relevant models is of great interest to many researchers. When multiple standards are in use, models are more readily used and re-used if there exist robust translators between the various accepted formats.

Summary: Antimony 2.4 and JSim 2.10 provide translation capabilities from their own formats to SBML and CellML. All provided unique challenges, stemming from differences in each format’s inherent design, in addition to differences in functionality.

Availability and implementation: Both programs are available under BSD licenses; Antimony from http://antimony.sourceforge.net/ and JSim from http://physiome.org/jsim/.

Contact:  lpsmith@u.washington.edu
PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra
Authors: Kertész-Farkas Attila , Reiz Beáta , Vera Roberto , Myers Michael P. , Pongor Sándor
Published: November 2013

Motivation: Tandem mass spectrometry has become a standard tool for identifying post-translational modifications (PTMs) of proteins. Algorithmic searches for PTMs from tandem mass spectrum data (MS/MS) tend to be hampered by noisy data as well as by a combinatorial explosion of search space. This leads to high uncertainty and long search-execution times.

Results: To address this issue, we present PTMTreeSearch, a new algorithm that uses a large database of known PTMs to identify PTMs from MS/MS data. For a given peptide sequence, PTMTreeSearch builds a computational tree wherein each path from the root to the leaves is labeled with the amino acids of a peptide sequence. Branches then represent PTMs. Various empirical tree pruning rules have been designed to decrease the search-execution time by eliminating biologically unlikely solutions. PTMTreeSearch first identifies a relatively small set of high confidence PTM types, and in a second stage, performs a more exhaustive search on this restricted set using relaxed search parameter settings. An analysis of experimental data shows that using the same criteria for false discovery, PTMTreeSearch annotates more peptides than the current state-of-the-art methods and PTM identification algorithms, and achieves this at roughly the same execution time. PTMTreeSearch is implemented as a plugable scoring function in the X!Tandem search engine.

Availability: The source code of PTMTreeSearch and a demo server application can be found at http://net.icgeb.org/ptmtreesearch.

Contacts:  pongor@icgeb.org

Supplementary information:  Supplementary materials are available at Bioinformatics online.
Bayesian network prior: network analysis of biological data using external knowledge
Authors: Isci Senol , Dogan Haluk , Ozturk Cengizhan , Otu Hasan H.
Published: November 2013

Motivation: Reverse engineering GI networks from experimental data is a challenging task due to the complex nature of the networks and the noise inherent in the data. One way to overcome these hurdles would be incorporating the vast amounts of external biological knowledge when building interaction networks. We propose a framework where GI networks are learned from experimental data using Bayesian networks (BNs) and the incorporation of external knowledge is also done via a BN that we call Bayesian Network Prior (BNP). BNP depicts the relation between various evidence types that contribute to the event ‘gene interaction’ and is used to calculate the probability of a candidate graph (G) in the structure learning process.

Results: Our simulation results on synthetic, simulated and real biological data show that the proposed approach can identify the underlying interaction network with high accuracy even when the prior information is distorted and outperforms existing methods.

Availability: Accompanying BNP software package is freely available for academic use at http://bioe.bilgi.edu.tr/BNP.

Contact:  hasan.otu@bilgi.edu.tr

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors
Authors: Wilson Mandy L. , Okumoto Sakiko , Adam Laura , Peccoud Jean
Published: November 2013

Motivation: Expression vectors used in different biotechnology applications are designed with domain-specific rules. For instance, promoters, origins of replication or homologous recombination sites are host-specific. Similarly, chromosomal integration or viral delivery of an expression cassette imposes specific structural constraints. As de novo gene synthesis and synthetic biology methods permeate many biotechnology specialties, the design of application-specific expression vectors becomes the new norm. In this context, it is desirable to formalize vector design strategies applicable in different domains.

Results: Using the design of constructs to express genes in the chloroplast of Chlamydomonas reinhardtii as an example, we show that a vector design strategy can be formalized as a domain-specific language. We have developed a graphical editor of context-free grammars usable by biologists without prior exposure to language theory. This environment makes it possible for biologists to iteratively improve their design strategies throughout the course of a project. It is also possible to ensure that vectors designed with early iterations of the language are consistent with the latest iteration of the language.

Availability and implementation: The context-free grammar editor is part of the GenoCAD application. A public instance of GenoCAD is available at http://www.genocad.org. GenoCAD source code is available from SourceForge and licensed under the Apache v2.0 open source license.

Contact: peccoud@vt.edu

Supplementary Information: Supplementary data are available at Bioinformatics online.
Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing
Authors: Doi Koichiro , Monjo Taku , Hoang Pham H. , Yoshimura Jun , Yurino Hideaki , Mitsui Jun , Ishiura Hiroyuki , Takahashi Yuji , Ichikawa Yaeko , Goto Jun , Tsuji Shoji , Morishita Shinichi
Published: November 2013

Motivation: Long expansions of short tandem repeats (STRs), i.e. DNA repeats of 2–6 nt, are associated with some genetic diseases. Cost-efficient high-throughput sequencing can quickly produce billions of short reads that would be useful for uncovering disease-associated STRs. However, enumerating STRs in short reads remains largely unexplored because of the difficulty in elucidating STRs much longer than 100 bp, the typical length of short reads.

Results: We propose ab initio procedures for sensing and locating long STRs promptly by using the frequency distribution of all STRs and paired-end read information. We validated the reproducibility of this method using biological replicates and used it to locate an STR associated with a brain disease (SCA31). Subsequently, we sequenced this STR site in 11 SCA31 samples using SMRTTM sequencing (Pacific Biosciences), determined 2.3–3.1 kb sequences at nucleotide resolution and revealed that (TGGAA)- and (TAAAATAGAA)-repeat expansions determined the instability of the repeat expansions associated with SCA31. Our method could also identify common STRs, (AAAG)- and (AAAAG)-repeat expansions, which are remarkably expanded at four positions in an SCA31 sample. This is the first proposed method for rapidly finding disease-associated long STRs in personal genomes using hybrid sequencing of short and long reads.

Availability and implementation: Our TRhist software is available at http://trhist.gi.k.u-tokyo.ac.jp/.

Contact:  moris@cb.k.u-tokyo.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.
RNAseqViewer: visualization tool for RNA-Seq data
Authors: Rogé Xavier , Zhang Xuegong
Published: November 2013

Summary: With the advances of RNA sequencing technologies, scientists need new tools to analyze transcriptome data. We introduce RNAseqViewer, a new visualization tool dedicated to RNA-Seq data. The program offers innovative ways to represent transcriptome data for single or multiple samples. It is a handy tool for scientists who use RNA-Seq data to compare multiple transcriptomes, for example, to compare gene expression and alternative splicing of cancer samples or of different development stages.

Availability and implementation: RNAseqViewer is freely available for academic use at http://bioinfo.au.tsinghua.edu.cn/software/RNAseqViewer/

Contact: zhangxg@tsinghua.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.
A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences
Authors: Sreeskandarajan Sutharzan , Flowers Michelle M. , Karro John E. , Liang Chun
Published: November 2013

Summary: Palindromic sequences, or inverted repeats (IRs), in DNA sequences involve important biological processes such as DNA–protein binding, DNA replication and DNA transposition. Development of bioinformatics tools that are capable of accurately detecting perfect IRs can enable genome-wide studies of IR patterns in both prokaryotes and eukaryotes. Different from conventional string-comparison approaches, we propose a novel algorithm that uses a cumulative score system based on a prime number representation of nucleotide bases. We then implemented this algorithm as a MATLAB-based program for perfect IR detection. In comparison with other existing tools, our program demonstrates a high accuracy in detecting nested and overlapping IRs.

Availability and implementation: The source code is freely available on (http://bioinfolab.miamioh.edu/bioinfolab/palindrome.php)

Contact:  liangc@miamioh.edu or karroje@miamioh.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
RelateAdmix: a software tool for estimating relatedness between admixed individuals
Authors: Moltke Ida , Albrechtsen Anders
Published: November 2013

Motivation: Pairwise relatedness plays an important role in a range of genetic research fields. However, currently only few estimators exist for individuals that are admixed, i.e. have ancestry from more than one population, and these estimators fail in some situations.

Results: We present a new software tool, RelateAdmix, for obtaining maximum likelihood estimates of pairwise relatedness from genetic data between admixed individuals. We show using simulated data that it gives rise to better estimates than three state-of-the-art software tools, REAP, KING and Plink, while still being fast enough to be applicable to large datasets.

Availability and implementation: The software tool, implemented in C and R, is freely available from www.popgen.dk/software.

Contact:  albrecht@binf.ku.dk

Supplementary information:  Supplementary data are available at Bioinformatics online.
AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations
Authors: Vuong Hue , Stephens Robert M. , Volfovsky Natalia
Published: November 2013

Motivation: The plethora of information that emerges from large-scale genome characterization studies has triggered the development of computational frameworks and tools for efficient analysis, interpretation and visualization of genomic data. Functional annotation of genomic variations and the ability to visualize the data in the context of whole genome and/or multiple genomes has remained a challenging task. We have developed an interactive web-based tool, AVIA (Annotation, Visualization and Impact Analysis), to explore and interpret large sets of genomic variations (single nucleotide variations and insertion/deletions) and to help guide and summarize genomic experiments. The annotation, summary plots and tables are packaged and can be downloaded by the user from the email link provided.

Availability and implementation:   http://avia.abcc.ncifcrf.gov.

Contact:   vuonghm@mail.nih.gov

Supplementary information:   Supplementary data are available at Bioinformatics online.
HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences
Authors: Matias Rodrigues João F. , von Mering Christian
Published: November 2013

Motivation: Nucleotide sequence data are being produced at an ever increasing rate. Clustering such sequences by similarity is often an essential first step in their analysis—intended to reduce redundancy, define gene families or suggest taxonomic units. Exact clustering algorithms, such as hierarchical clustering, scale relatively poorly in terms of run time and memory usage, yet they are desirable because heuristic shortcuts taken during clustering might have unintended consequences in later analysis steps.

Results: Here we present HPC-CLUST, a highly optimized software pipeline that can cluster large numbers of pre-aligned DNA sequences by running on distributed computing hardware. It allocates both memory and computing resources efficiently, and can process more than a million sequences in a few hours on a small cluster.

Availability and implementation: Source code and binaries are freely available at http://meringlab.org/software/hpc-clust/; the pipeline is implemented in C++ and uses the Message Passing Interface (MPI) standard for distributed computing.

Contact:   mering@imls.uzh.ch

Supplementary Information:   Supplementary data are available at Bioinformatics online.
Addressing the Mandate for Hand-off Education
Authors: Lane-Fall Meghan B. , Brooks Amber K. , Wilkins Sara A. , Davis Joshua J. , Riesenberg Lee Ann
Published: November 2013

The Accreditation Council for Graduate Medical Education requires that residency programs teach residents about handoffs and ensure their competence in this communication skill. Development of hand-off curricula for anesthesia residency programs is hindered by the paucity of evidence regarding how to conduct, teach, and evaluate handoffs in the various settings where anesthesia practitioners work. This narrative review draws from literature in anesthesia and other disciplines to provide recommendations for anesthesia resident hand-off curriculum development and evaluation.
Parental Influence on a Child's Autistic Traits
Authors: Phelps Randall , Nickel Robert , Eisert Debi , Stein Martin T.
Published: November 2013

CASE: Robbie is a 4-year-old boy whose parents are concerned about his speech, social skills, and repetitive behaviors. He has poor articulation; at time, he is difficult to understand. On the other hand, he has a fair vocabulary, and he has good intent to communicate. He is generally able to communicate his needs and wants. He likes to tell his parents about his day.

When he begins the day at preschool, Robbie initially stands by himself and watches. He slowly warms up and eventually participates in activities. He engages in parallel play or follows other children. He knows names of children at preschool, and he is well liked. He is affectionate with his parents.

When Robbie is excited, he wiggles his fingers, flaps his arms, and grimaces. He can be quite rigid; for example, he gets very distressed when his mother sets his cup down on his right side instead of his left. However, in general, Robbie has a sunny personality. He likes to watch children's television shows. He pretends plays with action figures. Robbie is an only child who lives with both parents. His mother works full-time, and his father is in home with Robbie during the day.

When examined in the office, Robbie had a bright affect, good eye contact, and social referencing. He demonstrated good communicative intent, but poor articulation and some jargoning. He frequently wiggled his fingers and flapped his hands with excitement. Robbie had a borderline score on the Autism Diagnostic Observation Schedule.

During the visit, the pediatrician noted that Robbie's father was rather quiet and rarely responded to questions. When he did respond, he had a monotone quality to his voice. He maintained either a flat or nervous affect throughout the visit. He made limited eye contact, and occasionally he stared excessively.
Land-use change and solar energy production: a real option approach
Authors: Gazheli Ardjan , Di Corato Luca
Published: November 2013

Purpose

– In this paper, a real option model is developed to examine the critical factors affecting the decision to lease agricultural land to a company installing a PV power plant. Subsidies introduced by governments for the production of renewable energies have increased the investments in this sector. Since ground-based solar cells need land for energy production, then potential trade-off with agriculture in terms of land exists. The paper aims to discuss these issues.

Design/methodology/approach

– The paper uses the real option approach in order to take into account for uncertainty and irreversibility of the farmer's decision.

Findings

– By applying the model to the province of Bologna (Italy), the paper illustrates the possible land-use change scenarios in this area. The paper concludes by discussing the importance of PV energy production as a source of income for farmers and its implications from a social perspective.

Originality/value

– The research is applied to the province of Bologna (Italy) where investments in ground-based solar cells are becoming quite common. The originality lies in the fact of considering the investment as irreversible, since it is a 20-year commitment from the farmers. The paper also takes into account the uncertainty in agricultural commodities' prices.
Real options or net present value?
Authors: Tubetov Dulat , Christin Maart-Noelck Syster , Musshoff Oliver
Published: November 2013

Purpose

– The purposes of the study are to compare the investment behavior of farmers in Kazakhstan as a transforming country and in Germany as a Western industrialized country as well as to analyze whether the investment behavior of farmers is consistent with the normative benchmarks of the net present value approach or the real options (RO) approach.

Design/methodology/approach

– The paper conducted an experiment with 100 Kazakhstani and 106 German farmers. The first part of the experiment describes an investment opportunity in an agricultural and in a non-agricultural treatment. The second part refers to a Holt and Laury lottery to determine farmers' risk attitude that could influence the investment behavior.

Findings

– The results show that both approaches do not provide an exact prediction of the investment behavior of farmers. However, German farmers invest later than Kazakhstani farmers meaning that the investment behavior of German farmers is closer to the RO approach. This might imply that German farmers are more likely to take into account the value of flexibility when making investment decisions than Kazakhstani farmers.

Research limitations/implications

– Since investment behavior is country-specific, it is worth investigating whether farmers from other transforming countries would show different investment behavior compared to farmers from other Western industrialized countries. Furthermore, decision-making behavior related to investments could be different from that related to disinvestments. Therefore, it may be interesting to analyze the disinvestment decisions of farmers in transforming and Western industrialized countries.

Practical implications

– The results show that it is not acceptable to apply the results of experiments investigating the investment behavior of entrepreneurs in a transforming country to entrepreneurs in a Western industrialized country and vice versa. Furthermore, training for farmers is needed because there is still room for improvement in order to achieve the RO benchmark. Finally, taking into account RO effects could improve the results of policy impact analysis.

Originality/value

– This is the first experimental study comparing the investment behavior of farmers from a transforming country and from a Western industrialized country.
After the disaster
Authors: Osborne Danny , G. Sibley Chris
Published: November 2013

Purpose

– The purpose of this paper is to examine individual differences in people's resilience to changes in psychological distress following the 22 February 2011 Christchurch earthquake.

Design/methodology/approach

– Data were based on a subsample of the New Zealand Attitudes and Values Study (NZAVS) – an annual nation-wide longitudinal study of New Zealand adults that began in 2009. In both waves of the NZAVS examined here, participants completed measures of the Big-Five, psychological distress, and demographic covariates. As such, the analyses, which focus on participants who were living in the Canterbury region before the 2011 earthquake (n=325), use measures of personality collected in late October of 2010 (Time 1) to predict changes in psychological distress after the devastation that unfolded on 22 February 2011.

Findings

– Time 1 levels of Emotional Stability were inversely associated with increases in psychological distress following the 2011 earthquake. Psychological distress assessed at Time 1, however, was uncorrelated with changes in Emotional Stability.

Practical implications

– These results show that Emotional Stability protects people against decrements to mental health following a disaster. Thus, efforts to rebuild disaster-stricken communities should ensure that those who are particularly likely to experience increases in psychological distress (i.e. those who, before a disaster, are low on Emotional Stability) receive the help they need.

Originality/value

– This study assesses a subsample of respondents from a longitudinally based national probability study to show that Emotional Stability exerts a cross-lagged effect on changes in psychological distress following a natural disaster. The access to such measures affords us the rare opportunity to explain how people cope in the wake of a catastrophic disaster.
Do governance factors matter for happiness in the MENA region?
Authors: Gholipour Fereidouni Hassan , Najdi Youhanna , Ekhtiari Amiri Reza
Published: November 2013

Purpose

– Unhappiness has been recognized as one of the main factors that cause political unrest in the Middle East and North Africa (MENA) region in recent years. The purpose of this study is to investigate the effects of governance matters on happiness in the MENA region while controlling for other relevant determinants.

Design/methodology/approach

– The paper applies panel random effects regression analyses by using data from 14 MENA countries over the period of 2009-2011.

Findings

– The empirical results show that higher level of political stability and absence of violence, government effectiveness and rule of law significantly increase happiness in the region. Furthermore, the paper finds that voice and accountability, regulatory quality and control of corruption variables have positive relationship with happiness but are not significant.

Originality/value

– Most studies in this area cover developed countries. Since findings for developed countries might not be directly transferable to emerging economies such as MENA countries, therefore, more work is necessary to obtain a clearer picture of the political determinants of happiness in this region.
The use of Facebook in tertiary education
Authors: Renee Staines Zoe , Lauchs Mark
Published: November 2013

Purpose

– This study aims to evaluate the usefulness of a university unit Facebook page, which was established to support a first-year university justice unit. The study pays particular regard to the Facebook page's impact on students learning outcomes and communications amongst students and between students and teaching staff.

Design/methodology/approach

– All students enrolled in the unit were asked to complete an online survey, which sought to determine whether they used the unit Facebook page and if so, the nature and extent of their use.

Findings

– The study found that the unit Facebook page was useful in achieving most learning objectives for the unit. This included enhancing students' knowledge and understanding of unit content, as well as their ability to critically analyse unit materials. Students also indicated that they found the Facebook page better than the university's central learning management system across a range of areas. It was particularly useful for facilitating unit-related discussions.

Research limitations/implications

– The survey results reported in this paper are based on a relatively small sample of students (n=67) from a first-year university justice unit. Future studies should seek to garner evidence from broader and larger samples that transcend specific unit populations. However, the findings of this study do indicate further support for the use of Facebook as a supplementary tool in university education.

Originality/value

– This study focuses on two aspects of social networking technologies that have not been previously researched and thus contributes to the growing literature on the uses and benefits of Facebook in tertiary education.
Is perception of leadership influenced by office environment?
Authors: Bodin Danielsson Christina , Wulff Cornelia , Westerlund Hugo
Published: November 2013

Purpose

– This explorative study aims to examine the impact of office type on employees' perception of managerial leadership, a largely unexplored area. A gender perspective is applied to examine whether women and men perceive leadership differently in different office types.

Design/methodology/approach

– Cross-sectional study is based on 5,358 office employees from the Swedish Longitudinal Occupational Study of Health in 2010. The employees worked in the seven different office types identified in contemporary office design: cell-offices, shared-room offices, small open plan offices, medium-sized open plan offices, large open plan offices, flex-offices, and combi-offices. Cell-office was used as reference in the analysis.

Findings

– Poorer ratings of leadership were found in shared-room offices, and better in medium-sized open plan offices. A tendency towards a gender difference in perceived leadership was found only in small open plan offices, which appear to be better for men and worse for women.

Practical implications

– The results suggest that the office environment has an influence on perceived managerial leadership. This means office design should be considered in relation to leadership style in order for an organization to be successful.

Originality/value

– To the authors' knowledge, no other study has investigated the relationship between office environment and managerial leadership.
New Zealand corporate boards in transition
Authors: Boyle Glenn , Ji Xu
Published: November 2013

Purpose

– The purpose of this paper is to uncover the stylised facts about NZ corporate boards and identify unanswered questions about their composition, activity and incentives during the 16-year period between 1995 and 2010.

Design/methodology/approach

– The paper uses annual report data to document the evolution of 22 NZ board characteristics. The paper also informally compares these trends with those occurring in other countries.

Findings

– Unsurprisingly, the representation of non-executive, independent and female directors on NZ boards rose during the period, as did real chair and director fees and the importance of board committees, while average board size fell. Perhaps more surprisingly, much of this movement occurred before NZX governance reforms in 2003. Moreover, there are some intriguing differences between New Zealand and other, mainly larger, countries.

Research limitations/implications

– The analysis is largely descriptive and focuses on identifying questions rather than answering them.

Originality/value

– The paper fills an obvious gap in the governance literature, which largely ignores small, open economies, and hence provides little clue as to the overall state and evolution of NZ boards. The paper also identifies a number of questions for further research.
Helping families to manage challenging behaviour after paediatric traumatic brain injury (TBI): a model approach and review of the literature
Authors: Thushara Woods Damith , Catroppa Cathy , Eren Senem , Godfrey Celia , A. Anderson Vicki
Published: November 2013

Purpose

– The purpose of this paper is to review and summarise a small but growing body of literature demonstrating that by embedding intervention within a family context offers the greatest promise of success in working with families caring for a child with traumatic brain injury (TBI).

Design/methodology/approach

– The approach takes the form of a literature review.

Findings

– The current family-centred evidence-based research indicates the potential benefits for the delivery of family focused interventions following childhood TBI.

Originality/value

– The paper adds to the paediatric TBI literature as being of the few papers to incorporate a number of novel family-centred behavioural interventions into the one review paper.
Species versus guild level differentiation revealed across the annual cycle by isotopic niche examination
Authors: Bodey Thomas W. , Ward Eric J. , Phillips Richard A. , McGill Rona A. R. , Bearhop Stuart
Published: November 2013

Interspecific competitive interactions typically result in niche differentiation to alleviate competition through mechanisms including character displacement. However, competition is not the sole constraint on resource partitioning, and its effects are mediated by factors including the environmental context in which species coexist.

Colonial seabirds provide an excellent opportunity to investigate the importance of competition in shaping realized niche widths because their life histories lead to variation in intra‐ and interspecific competition across the annual cycle. Dense breeding aggregations result in intense competition for prey in surrounding waters, whereas non‐breeding dispersal to larger geographical areas produces lower densities of competitors.

Bayesian hierarchical models of the isotopic niche, closely aligned to the trophic niche, reveal the degree of segregation between species and functional groups during both time periods. Surprisingly, species explained far more of the variance in the isotopic niche during the non‐breeding than the breeding period.

Our results underline the key role of non‐breeding dynamics in alleviating competition and promoting distinctions between species through the facilitation of resource partitioning. Such situations may be common in a diverse range of communities sustained by ephemeral but abundant food items.

This highlights how consideration of the hierarchical grouping of competitive interactions alongside consideration of abiotic constraints across the complete annual cycle allows a full understanding of the role of competition in driving patterns of character displacement.
EuropeanCommission merger control: Combining competition and the creation of largerEuropean firms
Authors: Thatcher Mark
Published: November 2013

The article examines theEuropeanCommission's use of its legal powers over mergers. It discusses and tests two views. One is that the ‘neoliberal’Commission has ended previous industrial policies of aiding ‘national champion’ firms to grow through mergers and instead pursues a ‘merger‐constraining’ policy of vigorously using its legal powers to block mergers. The other is that theCommission follows an ‘integrationist policy’ of seeking the development of largerEuropean firms to deepen economic integration. It examinesCommission decisions under the 1989ECMerger Regulation between 1990 and 2009. It selects three major sectors that are ‘likely’ for the ‘merger‐constraining’ view – banking, energy and telecommunications – and analyses a dataset of almost 600Commission decisions and then individual merger cases. It finds that theCommission has approved almost all mergers, including by former ‘national champion’ firms. There have been only two prohibitions over 20 years in the three sectors and the outcome has been the creation of largerEuropean firms through mergers. It explains how theCommission can pursue an integrationist policy through the application of competition processes and criteria. The wider implication is that theCommission can combine competition policy with achieving the ‘industrial policy’ aim of aiding the development of largerEuropean firms.
Anorectal malformations presenting with colorectal perforation: Frequency, associated morbidity and mortality
Authors: Eltayeb Almoutaz A
Published: November 2013

Aim

Colorectal perforations (CRP) in patients with anorectal malformations (ARM) are infrequently encountered because of their early diagnosis and treatment. Despite recently‐improved neonatal management; CRP during the neonatal period is still a major problem for paediatric surgeons. The aim of the present study was to evaluate the frequency of bowel perforation with ARM in our locality, and the associated morbidity and mortality.

Patients and Methods

During May 2002 and April 2012, a prospective study was conducted on 416 neonates suffering from ARM (277 high ARM, and 138 low ARM), who presented to Assiut University Children Hospital. The inclusion criteria were all neonates with CRP only related to acute obstruction caused by ARM.

Results

Only seven cases fulfilled the inclusion criteria. Their age at presentation ranged from 3 days to 14 days. Five neonates had high ARM, while two had low ARM. The diagnosis of bowel perforation was suspected preoperatively in four cases, and was accidentally discovered either intraoperatively in two cases with high ARM or after the anoplasty for low ARM. Two mortalities were encountered; both had a complicated postoperative course with postoperative sepsis and disseminated intravascular coagulation.

Conclusions

Although rare, colorectal perforation in ARM should always be suspected in delayed ARM presenters. Close postoperative observation is very important to detect any late postoperative perforation.
Bacteria abundance and diversity of different life stages of Plutella xylostella (Lepidoptera: Plutellidae), revealed by bacteria culture‐dependent and PCR‐DGGE methods
Authors: Lin Xiao‐Li , Pan Qin‐Jian , Tian Hong‐Gang , Douglas Angela E. , Liu Tong‐Xian
Published: November 2013

Microbial abundance and diversity of different life stages (fourth instar larvae, pupae and adults) of the diamondback moth, Plutella xylostella L., collected from field and reared in laboratory, were investigated using bacteria culture‐dependent method and PCR‐DGGE analysis based on the sequence of bacteria 16S rRNA V3 region gene. A large quantity of bacteria was found in all life stages of P. xylostella. Field population had higher quantity of bacteria than laboratory population, and larval gut had higher quantity than pupae and adults. Culturable bacteria differed in different life stages of P. xylostella. Twenty‐five different bacterial strains were identified in total, among them 20 strains were presented in larval gut, only 8 strains in pupae and 14 strains in adults were detected. Firmicutes bacteria, Bacillus sp., were the most dominant species in every life stage. 15 distinct bands were obtained from DGGE electrophoresis gel. The sequences blasted in GenBank database showed these bacteria belonged to six different genera. Phylogenetic analysis showed the sequences of the bacteria belonged to the Actinobacteri, Proteobacteria and Firmicutes. Serratia sp. in Proteobacteria was the most abundant species in larval gut. In pupae, unculturable bacteria were the most dominant species, and unculturable bacteria and Serratia sp. were the most dominant species in adults. Our study suggested that a combination of molecular and traditional culturing methods can be effectively used to analyze and to determine the diversity of gut microflora. These known bacteria may play important roles in development of P. xylostella.
Simplifying data acquisition in plant canopies‐ Measurements of leaf angles with a cell phone
Authors: Escribano‐Rocafort Adrián G. , Ventre‐Lespiaucq Agustina B. , Granado‐Yela Carlos , López‐Pintor Antonio , Delgado Juan A. , Muñoz Vicente , Dorado Gabriel A. , Balaguer Luis
Published: November 2013

Canopies are complex multilayered structures comprising individual plant crowns exposing a multifaceted surface area to sunlight. Foliage arrangement and properties are the main mediators of canopy functions. The leaves act as light traps whose exposure to sunlight varies with time of the day, date and latitude in a trade‐off between photosynthetic light harvesting and excessive or photoinhibitory light avoidance. To date, ecological research based upon leaf sampling has been limited by the available technology, with which data acquisition becomes labour intensive and time‐consuming, given the overwhelming number of leaves involved.

In the present study, our goal involved developing a tool capable of measuring a sufficient number of leaves to enable analysis of leaf populations, tree crowns and canopies. We specifically tested whether a cell phone working as a 3D pointer could yield reliable, repeatable and valid leaf angle measurements with a simple gesture. We evaluated the accuracy of this method under controlled conditions, using a 3D digitizer, and we compared performance in the field with the methods commonly used. We presented an equation to estimate the potential proportion of the leaf exposed to direct sunlight (SAL) at any given time and compared the results with those obtained by means of a graphical method.

We found a strong and highly significant correlation between the graphical methods and the equation presented. The calibration process showed a strong correlation between the results derived from the two methods with a mean relative difference below 10%. The mean relative difference in calculation of instantaneous exposure was below 5%. Our device performed equally well in diverse locations, in which we characterized over 700 leaves in a single day.

The new method, involving the use of a cell phone, is much more effective than the traditional methods or digitizers when the goal is to scale up from leaf position to performance of leaf populations, tree crowns or canopies. Our methodology constitutes an affordable and valuable tool within which to frame a wide range of ecological hypotheses and to support canopy modelling approaches.
Do Better Monitoring Institutions Increase Leadership Quality in Community Organizations? Evidence from Uganda
Authors: Grossman Guy , Hanlon W. Walker
Published: November 2013

We offer a framework for analyzing the impact of monitoring—a commonly recommended solution to poor leadership—on the quality of democratically elected leaders in community organizations in low‐income countries. In our model, groups may face a trade‐off between leader ability and effort. If the group's ability to monitor the leader is low, then the leader may exert too little effort. A higher level of monitoring increases leader effort, raising the value of the public good. However, more intense monitoring may also drive higher‐ability members to opt out of candidacy, reducing public‐goods value. The result is an inverted U‐shaped relationship between the level of monitoring and the value of the public good. The trade‐off between leader effort and ability, however, only exists in the presence of sufficient private‐income opportunities. These predictions are assessed using original data gathered from Ugandan farmer associations.
Adaptation Machines and the Parasitic Politics of Life in Jamaican Disaster Resilience
Authors: Grove Kevin J.
Published: November 2013

This paper unpacks a politics of life at the heart of community‐based disaster management to advance a new understanding of resilience politics. Through an institutional ethnography of participatory resilience programming in Kingston, Jamaica, I explore how staff in Jamaica's national disaster management agency engaged with a qualitatively distinct form of collective life in Kingston's garrison districts. Garrison life has been shaped by the confluence of political economic, cultural, geopolitical force relations, which creates a hyper‐adaptive life that exceeds the techniques and rationalities of neoliberal disaster resilience. I draw on autonomist Marxist and Deleuzian readings of biopolitics to identify a new subject of disaster politics that I call, after Deleuze and Guattari, “adaptation machines”, decentralized apparatuses of capture that are parasitically reliant on the population's immanent adaptive capacities. The concept of adaptation machines enables us to envision resilience politics as a struggle over how to appropriate vulnerable peoples’ world‐forming constituent power.
Oral sucrose and non‐nutritive sucking goes some way to reducing pain during retinopathy of prematurity eye examinations
Authors: Dilli Dilek , İlarslan Nisa Eda Çullas , Kabataş Emrah Utku , Zenciroğlu Ayşegül , Şimşek Yıldız , Okumuş Nurullah
Published: November 2013

Aim

To evaluate the efficacy of oral sucrose combined with non‐nutritive sucking for reducing pain associated with retinopathy of prematurity screening.

Methods

This was a randomised controlled study of 64 infants undergoing eye examination for retinopathy of prematurity screening. Topical anaesthetic (Proparacaine; Alcaine® drop 0.5%: ALCON CANADA Inc., Mississauga, Canada) was applied 30 sec before the eye examination in all infants. The infants in intervention group (Group 1, n = 32) received 0.5 mL/kg of 24% sucrose with a pacifier. The control group (Group 2, n = 32) received 0.5 mL/kg of sterile water with a pacifier.

Results

The groups had similar gestational ages (28.5 ± 2.8 weeks), mean birthweight (1304 ± 466 g) or corrected gestational age (35.4 ± 3.7 weeks) at examination. The intervention group had a significantly lower mean Premature Infant Pain Profile score during examination of the first eye, following insertion of the speculum (Group 1:13.7 ± 2.1 vs. Group 2:16.4 ± 1.8, p = 0.001).

Conclusion

Although sucrose combined with non‐nutritive sucking modestly reduces pain scores during eye examinations, there is need to further studies to explore significant pain relief for infants undergoing retinopathy of prematurity screening.
Kinematic gait analysis and lactation performance in dairy cows fed a diet supplemented with zinc, manganese, copper and cobalt
Authors: Yamamoto Satoshi , Ito Kazuhiko , Suzuki Kii , Matsushima Yuki , Watanabe Izumi , Watanabe Yutaka , Abiko Keima , Kamada Toshihiko , Sato Kan
Published: November 2013

This study investigated how supplementation of the diet of dairy cows with trace minerals (zinc, manganese, copper and cobalt) affected kinematic gait parameters and lactation performance. Eight Holstein cows were divided into two groups, with each group receiving a different dietary treatment (control diet, or control diet supplemented with trace minerals) in a two‐period crossover design. Kinematic gait parameters were calculated by using image analysis software. Compared to cows fed the control diet, cows that received the trace mineral‐supplemented diet exhibited significantly increased walking and stepping rates, and had a shorter stance duration. Feed intake and milk production increased in cows fed the trace mineral‐supplemented diet compared with control groups. The plasma manganese concentration was not different in control and experimental cows. In contrast, cobalt was only detected in the plasma of cows fed the supplemented diet. These results provide the first evidence that trace mineral supplementation of the diet of dairy cows affects locomotion, and that the associated gait changes can be detected by using kinematic gait analysis. Moreover, trace mineral supplementation improved milk production and only minimally altered blood and physiological parameters in dairy cows.