bluuebunny/crossref_metadata_2025 huggingface dataset:
Thy-1: Shade and sun for integrin signaling
Authors: Sedwick Caitlin
Published: October 2015

The GPI-anchored protein Thy-1 can both promote and inhibit integrin activity.
Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space
Authors: Kaushik Swati , Nair Anu G. , Mutt Eshita , Subramanian Hari Prasanna , Sowdhamini Ramanathan
Published: October 2015

Motivation: In the post-genomic era, automatic annotation of protein sequences using computational homology-based methods is highly desirable. However, often protein sequences diverge to an extent where detection of homology and automatic annotation transfer is not straightforward. Sophisticated approaches to detect such distant relationships are needed. We propose a new approach to identify deep evolutionary relationships of proteins to overcome shortcomings of the available methods.

Results: We have developed a method to identify remote homologues more effectively from any protein sequence database by using several cascading events with Hidden Markov Models (C-HMM). We have implemented clustering of hits and profile generation of hit clusters to effectively reduce the computational timings of the cascaded sequence searches. Our C-HMM approach could cover 94, 83 and 40% coverage at family, superfamily and fold levels, respectively, when applied on diverse protein folds. We have compared C-HMM with various remote homology detection methods and discuss the trade-offs between coverage and false positives.

Availability and implementation: A standalone package implemented in Java along with a detailed documentation can be downloaded from https://github.com/RSLabNCBS/C-HMM

Supplementary information: Supplementary data are available at Bioinformatics online.

Contact:  mini@ncbs.res.in
FogLight: an efficient matrix-based approach to construct metabolic pathways by search space reduction
Authors: Khosraviani Mehrshad , Saheb Zamani Morteza , Bidkhori Gholamreza
Published: October 2015

Motivation: A fundamental computational problem in the area of metabolic engineering is finding metabolic pathways between a pair of source and target metabolites efficiently. We present an approach, namely FogLight, for searching metabolic networks utilizing Boolean (AND-OR) operations represented in matrix notation to efficiently reduce the search space. This enables the enumeration of all pathways between metabolites that are too distant for the application of brute-force methods.

Results: Benchmarking tests run with FogLight show that it can reduce the search space by up to 98%, after which the accelerated search for high accurate results is guaranteed. Using FogLight, several pathways between eight given pairs of metabolites are found of which the pathways from CO2 to ethanol are specifically discussed. Additionally, in comparison with three path-finding tools, namely PHT, FMM and RouteSearch, FogLight can find shorter and more pathways for attempted source-target metabolite pairs.

Contact:  szamani@aut.ac.ir, gholamreza.bidkhori@vtt.fi

Supplementary information:  Supplementary data are available at Bioinformatics online.
I-PV: a CIRCOS module for interactive protein sequence visualization
Authors: Tanyalcin Ibrahim , Al Assaf Carla , Gheldof Alexander , Stouffs Katrien , Lissens Willy , Jansen Anna C.
Published: October 2015

Summary: Today’s genome browsers and protein databanks supply vast amounts of information about proteins. The challenge is to concisely bring together this information in an interactive and easy to generate format.

Availability and implementation: We have developed an interactive CIRCOS module called i-PV to visualize user supplied protein sequence, conservation and SNV data in a live presentable format. I-PV can be downloaded from http://www.i-pv.org.

Contact:  ibrahim.tanyalcin@i-pv.org, itanyalc@vub.ac.be or support@i-pv.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic
Authors: Brown Peter , Pullan Wayne , Yang Yuedong , Zhou Yaoqi
Published: October 2015

Motivation: The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique.

Results: The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments.

Availability and implementation: SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org

Contact: yaoqi.zhou@griffith.edu.au
FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition
Authors: Wang Chao , Zhang Haicang , Zheng Wei-Mou , Xu Dong , Zhu Jianwei , Wang Bing , Ning Kang , Sun Shiwei , Li Shuai Cheng , Bu Dongbo
Published: October 2015

Summary: The protein structure prediction approaches can be categorized into template-based modeling (including homology modeling and threading) and free modeling. However, the existing threading tools perform poorly on remote homologous proteins. Thus, improving fold recognition for remote homologous proteins remains a challenge. Besides, the proteome-wide structure prediction poses another challenge of increasing prediction throughput.

In this study, we presented FALCON@home as a protein structure prediction server focusing on remote homologue identification. The design of FALCON@home is based on the observation that a structural template, especially for remote homologous proteins, consists of conserved regions interweaved with highly variable regions. The highly variable regions lead to vague alignments in threading approaches. Thus, FALCON@home first extracts conserved regions from each template and then aligns a query protein with conserved regions only rather than the full-length template directly. This helps avoid the vague alignments rooted in highly variable regions, improving remote homologue identification.

We implemented FALCON@home using the Berkeley Open Infrastructure of Network Computing (BOINC) volunteer computing protocol. With computation power donated from over 20 000 volunteer CPUs, FALCON@home shows a throughput as high as processing of over 1000 proteins per day. In the Critical Assessment of protein Structure Prediction (CASP11), the FALCON@home-based prediction was ranked the 12th in the template-based modeling category. As an application, the structures of 880 mouse mitochondria proteins were predicted, which revealed the significant correlation between protein half-lives and protein structural factors.

Availability and implementation: FALCON@home is freely available at http://protein.ict.ac.cn/FALCON/.

Contact:  shuaicli@cityu.edu.hk, dbu@ict.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
miTRATA: a web-based tool for microRNA Truncation and Tailing Analysis
Authors: Patel Parth , Ramachandruni S. Deepthi , Kakrana Atul , Nakano Mayumi , Meyers Blake C.
Published: October 2015

Summary: We describe miTRATA, the first web-based tool for microRNA Truncation and Tailing Analysis—the analysis of 3′ modifications of microRNAs including the loss or gain of nucleotides relative to the canonical sequence. miTRATA is implemented in Python (version 3) and employs parallel processing modules to enhance its scalability when analyzing multiple small RNA (sRNA) sequencing datasets. It utilizes miRBase, currently version 21, as a source of known microRNAs for analysis. miTRATA notifies user(s) via email to download as well as visualize the results online. miTRATA’s strengths lie in (i) its biologist-focused web interface, (ii) improved scalability via parallel processing and (iii) its uniqueness as a webtool to perform microRNA truncation and tailing analysis.

Availability and implementation: miTRATA is developed in Python and PHP. It is available as a web-based application from https://wasabi.dbi.udel.edu/∼apps/ta/.

Contact:  meyers@dbi.udel.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data
Authors: Silva Genivaldo Gueiros Z. , Green Kevin T. , Dutilh Bas E. , Edwards Robert A.
Published: October 2015

Summary: Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools.

Availability and implementation: SUPER-FOCUS was implemented in Python, and its source code and the tool website are freely available at https://edwards.sdsu.edu/SUPERFOCUS.

Contact:  redwards@mail.sdsu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Automatic semantic classification of scientific literature according to the hallmarks of cancer
Authors: Baker Simon , Silins Ilona , Guo Yufan , Ali Imran , Högberg Johan , Stenius Ulla , Korhonen Anna
Published: October 2015

Motivation: The hallmarks of cancer have become highly influential in cancer research. They reduce the complexity of cancer into 10 principles (e.g. resisting cell death and sustaining proliferative signaling) that explain the biological capabilities acquired during the development of human tumors. Since new research depends crucially on existing knowledge, technology for semantic classification of scientific literature according to the hallmarks of cancer could greatly support literature review, knowledge discovery and applications in cancer research.

Results: We present the first step toward the development of such technology. We introduce a corpus of 1499 PubMed abstracts annotated according to the scientific evidence they provide for the 10 currently known hallmarks of cancer. We use this corpus to train a system that classifies PubMed literature according to the hallmarks. The system uses supervised machine learning and rich features largely based on biomedical text mining. We report good performance in both intrinsic and extrinsic evaluations, demonstrating both the accuracy of the methodology and its potential in supporting practical cancer research. We discuss how this approach could be developed and applied further in the future.

Availability and implementation: The corpus of hallmark-annotated PubMed abstracts and the software for classification are available at: http://www.cl.cam.ac.uk/∼sb895/HoC.html .

Contact:  simon.baker@cl.cam.ac.uk
CSSSCL: a python package that uses combined sequence similarity scores for accurate taxonomic classification of long and short sequence reads
Authors: Borozan Ivan , Ferretti Vincent
Published: October 2015

Summary: Sequence comparison of genetic material between known and unknown organisms plays a crucial role in genomics, metagenomics and phylogenetic analysis. The emerging long-read sequencing technologies can now produce reads of tens of kilobases in length that promise a more accurate assessment of their origin. To facilitate the classification of long and short DNA sequences, we have developed a Python package that implements a new sequence classification model that we have demonstrated to improve the classification accuracy when compared with other state of the art classification methods. For the purpose of validation, and to demonstrate its usefulness, we test the combined sequence similarity score classifier (CSSSCL) using three different datasets, including a metagenomic dataset composed of short reads.

Availability and implementation: Package’s source code and test datasets are available under the GPLv3 license at https://github.com/oicr-ibc/cssscl.

Contact:  ivan.borozan@oicr.on.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Jflow: a workflow management system for web applications
Authors: Mariette Jérôme , Escudié Frédéric , Bardou Philippe , Nabihoudine Ibouniyamine , Noirot Céline , Trotard Marie-Stéphane , Gaspin Christine , Klopp Christophe
Published: October 2015

Summary: Biologists produce large data sets and are in demand of rich and simple web portals in which they can upload and analyze their files. Providing such tools requires to mask the complexity induced by the needed High Performance Computing (HPC) environment. The connection between interface and computing infrastructure is usually specific to each portal. With Jflow, we introduce a Workflow Management System (WMS), composed of jQuery plug-ins which can easily be embedded in any web application and a Python library providing all requested features to setup, run and monitor workflows.

Availability and implementation: Jflow is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/jflow. The package is coming with full documentation, quick start and a running test portal.

Contact:  Jerome.Mariette@toulouse.inra.fr
Seascape genetics of saithe (Pollachius virens) across the North Atlantic using single nucleotide polymorphisms
Authors: Saha Atal , Hauser Lorenz , Kent Matthew , Planque Benjamin , Neat Francis , Kirubakaran Tina Graceline , Huse Irene , Homrum Eydna Í. , Fevolden Svein-Erik , Lien Sigbjørn , Johansen Torild
Published: October 2015

The identification of isolated populations in widely distributed marine species is often impeded by low levels of genetic differentiation. However, modern genetic approaches now allow for the efficient detection of potentially large numbers of novel genetic variations, thereby improving the power to identify biologically meaningful management units. To investigate the genetic structuring of saithe (Pollachius virens L.), we applied seascape genetic approaches to 131 single nucleotide polymorphism loci genotyped in 584 fish collected from 11 locations across the North Atlantic. Wombling analysis and the Monmonier algorithm revealed four genetic clusters (Barents Sea, Central Northeast Atlantic, Rockall, and Canada) across the species distribution range. These results imply that genetic structuring in saithe may be influenced by abiotic factors such as geographical distance, and bathymetry as well as biotic factors such as sex-biased migration, and natal homing. The results suggest a potential mismatch between management and biological units across the Northeast Atlantic, which may have implications for sustainable exploitation of the species.
Intuitionistic ancestral logic
Authors: Cohen Liron , Constable Robert L
Published: October 2015

In this article we define pure intuitionistic Ancestral Logic ( iAL ), extending pure intuitionistic First-Order Logic ( iFOL ). This logic is a dependently typed abstract programming language with computational functionality beyond iFOL given by its realizer for the transitive closure, TC . We derive this operator from the natural type theoretic definition of TC using intersection. We show that provable formulas in iAL are uniformly realizable, thus iAL is sound with respect to constructive type theory. We further show that iAL subsumes Kleene Algebras with tests and thus serves as a natural programming logic for proving properties of program schemes. We also extract schemes from proofs that iAL specifications are solvable.
Continuing Decline in Varicella Incidence After the 2-Dose Vaccination Recommendation—Connecticut, 2009–2014
Authors: Mullins Jocelyn , Kudish Kathy , Sosa Lynn , Hadler Jim
Published: October 2015

Background.  Varicella is a highly contagious vaccine-preventable illness. In 1996, the Advisory Committee for Immunization Practices recommended 1 dose of vaccine for children, and in 2006 it recommended 2 doses; Connecticut required 1 dose for school entry in 2000 and 2 doses for school entry starting in 2011. Connecticut varicella incidence overall and among persons aged 1–14 years declined during 2005–2008. We analyzed varicella surveillance data for 2009–2014 to characterize overall and age group-specific trends in the setting of the 2-dose requirement.

Methods.  Passive surveillance was used to collect data and identify incidence trends and changes in proportions, and these were assessed by χ2 tests for trend and proportion, respectively.

Results.  Varicella incidence decreased from 13.8 cases/100 000 persons during 2009 to 5.1 cases/100 000 persons during 2014 (P < .001); significant declines in incidence occurred among children aged 1–4, 5–9, and 10–14 years (P < .01 for each age group). Cases classified as preventable decreased from 44% during 2009 to 25% during 2014 (P < .01); significant declines in percentages of preventable cases occurred only among those aged 5–9 years (P < .05) and 10–14 (P < .01) years.

Conclusions.  Varicella incidence continued to decline in Connecticut in the setting of the 2-dose school-entry program. Continued surveillance is needed to assess the full influence of the 2-dose recommendation.
Detection of universality of dark matter profile from Subaru weak lensing measurements of 50 massive clusters
Authors: Niikura Hiroko , Takada Masahiro , Okabe Nobuhiro , Martino Rossella , Takahashi Ryuichi
Published: October 2015

We develop a novel method of measuring the lensing distortion profiles of clusters by stacking the “scaled” amplitudes of background galaxy ellipticities as a function of the “scaled” centric radius according to the Navarro–Frenk–White (NFW) prediction of each cluster, based on the assumption that the different clusters in a sample follow the universalNFW profile. First we demonstrate the feasibility of this method using both the analytical NFW model and simulated halos in a suite of high-resolution N-body simulations. We then apply, as a proof of concept, this method to the Subaru weak lensing data and the XMM/Chandra X-ray observables for a sample of 50 massive clusters in the redshift range 0.15 ≤ z ≤ 0.3, where their halo masses differ from each other by up to a factor of 10. To estimate the NFW parameters of each cluster, we use the halo mass proxy relation of X-ray observables, based on either the hydrostatic equilibrium or the gas mass, and then infer the halo concentration from the model scaling relation of halo concentration with halo mass. We evaluate the performance of the NFW scaling analysis by measuring the scatters of 50 cluster lensing profiles relative to the NFW predictions over a range of radii, 0.14 ≤ R/[h−1 Mpc] ≤ 2.8. We found 4–6 σ-level evidence of the universal NFW profile in 50 clusters, for both the X-ray halo mass proxy relations, although the gas mass appears to be a better proxy of the underlying true mass. By comparing the measurements with the simulations of cluster lensing profiles taking into account the statistical errors of intrinsic galaxy shapes in the Subaru data, we argue that additional halo mass errors or intrinsic scatters of σ(M500c)/M500c ∼ 0.2–0.3 could reconcile the difference between measurements and simulations. This method allows us to some extent to preserve characteristics of individual clusters in the statistical weak lensing analysis, thereby yielding a new means of exploiting the underlying genuine form of the halo mass profile and the halo mass proxy relations via weak lensing information, under the assumption of the existence of the universal profile.
OsGF14b Positively Regulates Panicle Blast Resistance but Negatively Regulates Leaf Blast Resistance in Rice
Authors: Liu Qing , Yang Jianyuan , Zhang Shaohong , Zhao Junliang , Feng Aiqing , Yang Tifeng , Wang Xiaofei , Mao Xinxue , Dong Jingfang , Zhu Xiaoyuan , Leung Hei , Leach Jan E. , Liu Bin
Published: October 2015

Although 14-3-3 proteins have been reported to be involved in responses to biotic stresses in plants, their functions in rice blast, the most destructive disease in rice, are largely unknown. Only GF14e has been confirmed to negatively regulate leaf blast. We report that GF14b is highly expressed in seedlings and panicles during blast infection. Rice plants overexpressing GF14b show enhanced resistance to panicle blast but are susceptible to leaf blast. In contrast, GF14b-silenced plants show increased susceptibility to panicle blast but enhanced resistance to leaf blast. Yeast one-hybrid assays demonstrate that WRKY71 binds to the promoter of GF14b and modulates its expression. Overexpression of GF14b induces expression of jasmonic acid (JA) synthesis-related genes but suppresses expression of salicylic acid (SA) synthesis-related genes. In contrast, suppressed GF14b expression causes decreased expression of JA synthesis-related genes but activation of SA synthesis-related genes. These results suggest that GF14b positively regulates panicle blast resistance but negatively regulates leaf blast resistance, and that GF14b-mediated disease resistance is associated with the JA- and SA-dependent pathway. The different functions for 14-3-3 proteins in leaf and panicle blast provide new evidence that leaf and panicle blast resistance are controlled by different mechanisms.
RAD Capture (Rapture): Flexible and efficient sequence-based genotyping
Authors: Ali Omar A. , O’Rourke Sean M. , Amish Stephen J. , Meek Mariah H. , Luikart Gordon , Jeffres Carson , Miller Michael R.
Published: October 2015

Massively parallel sequencing has revolutionized many areas of biology but sequencing large amounts of DNA in many individuals is cost-prohibitive and unnecessary for many studies. Genomic complexity reduction techniques such as sequence capture and restriction enzyme-based methods enable the analysis of many more individuals per unit cost. Despite their utility, current complexity reduction methods have limitations, especially when large numbers of individuals are analyzed. Here we develop a much improved restriction site associated DNA (RAD) sequencing protocol and a new method called Rapture (RAD capture). The new RAD protocol improves versatility by separating RAD tag isolation and sequencing library preparation into two distinct steps. This protocol also recovers more unique (non-clonal) RAD fragments which improves both standard RAD and Rapture analysis. Rapture then uses an in-solution capture of chosen RAD tags to target sequencing reads to desired loci. Rapture combines the benefits of both RAD and sequence capture, i.e. very inexpensive and rapid library preparation for many individuals as well as high specificity in the number and location of genomic loci analyzed. Our results demonstrate that Rapture is a rapid and flexible technology capable of analyzing a very large number of individuals with minimal sequencing and library preparation cost. The methods presented here should improve the efficiency of genetic analysis for many aspects of agricultural, environmental, and biomedical science.
Integrated analysis of oral tongue squamous cell carcinoma identifies key variants and pathways linked to risk habits, HPV, clinical parameters and tumor recurrence
Authors: Krishnan Neeraja M , Gupta Saurabh , Palve Vinayak , Varghese Linu , Pattnaik Swetansu , Jain Prachi , Khyriem Costerwell , Hariharan Arun K , Dhas Kunal , Nair Jayalakshmi , Pareek Manisha , Prasad Venkatesh K , Siddappa Gangotri , Suresh Amritha , Kekatpure Vikram D , Kuriakose Moni Abraham , Panda Binay
Published: October 2015

Oral tongue squamous cell carcinomas (OTSCC) are a homogenous group of tumors characterized by aggressive behavior, early spread to lymph nodes and a higher rate of regional failure. Additionally, the incidence of OTSCC among younger population (<50yrs) is on a rise; many of who lack the typical associated risk factors of alcohol and/or tobacco exposure. We present data on SNVs, indels, regions with LOH, and CNVs from fifty-paired oral tongue primary tumors and link the significant somatic variants with clinical parameters, epidemiological factors including HPV infection and tumor recurrence. Apart from the frequent somatic variants harbored inTP53, CASP8, RASA1, NOTCHandCDKN2Agenes, significant amplifications and/or deletions were detected in chromosomes 6-9, and 11 in the tumors. Variants inCASP8andCDKN2Awere mutually exclusive.CDKN2A, P1K3CA, RASA1andDMDvariants were exclusively linked to smoking, chewing, HPV infection and tumor stage. We also performed whole-genome gene expression study that identified matrix metalloproteases to be highly expressed in tumors and linked pathways involving arachidonic acid and NF-κ-B to habits and distant metastasis, respectively. Functional knockdown studies in cell lines demonstrated the role ofCASP8in HPV-negative OTSCC cell line. Finally, we identified a 38-gene minimal signature that predicts tumor recurrence using an ensemble machine learning method. Taken together, this study links molecular signatures to various clinical and epidemiological factors in a homogeneous tumor population with a relatively high HPV prevalence.
Privacy as a secondary goal problem: an experiment examining control
Authors: Hughes-Roberts Thomas
Published: October 2015

Purpose

– The purpose of this paper is to report on results of an investigation into the impact of adding privacy salient information (defined through the theory of planned behaviour) into the user interface (UI) of a faux social network.

Design/methodology/approach

– Participants were asked to create their profiles on a new social network specifically for Nottingham Trent University students by answering a series of questions that vary in the sensitivity of personal information requested. A treatment is designed that allows participants to review their answers and make amendments based on suggestions from the treatment. A dynamic privacy score that improves as amendments are made is designed to encourage privacy-oriented behaviour. Results from the treatment group are compared to a control group.

Findings

– Participants within the treatment group disclosed less than those in the control with statistical significance. The more sensitive questions in particular were answered less when compared to the control, suggesting that participants were making more privacy-conscious decisions.

Practical implications

– Work within this paper suggests that simple UI changes can promote more privacy-conscious behaviour. These simple changes could provide a low-cost method to ensuring the Internet safety of a wide range of users.

Originality/value

– This study provides a clear definition of privacy salient UI mechanisms based on a well-established theory of behaviour and examines their potential effect on end-users through a novel experiment. Results and methods from this work can enable researchers to better understand privacy behaviour.
Exploring the relationship between student mobile information security awareness and behavioural intent
Authors: Ngoqo Bukelwa , Flowerday Stephen V.
Published: October 2015

Purpose

– The purpose of this paper was to analyse existing theories from the social sciences to gain a better understanding of factors which contribute to student mobile phone users’ poor information security behaviour. Two key aspects associated with information security behaviour were considered, namely, awareness and behavioural intent. This paper proposes that the knowing-and-doing gap can possibly be reduced by addressing both awareness and behavioural intent. This research paper explores the relationship between student mobile phone user information security awareness and behavioural intent in a developmental university in South Africa.

Design/methodology/approach

– Information security awareness interventions were implemented in this action research study, and student information security behavioural intent was observed after each cycle.

Findings

– The poor security behaviour exhibited by student mobile phone users, which was confirmed by the findings of this study, is of particular interest in the university context, as most undergraduate students are offered a computer-related course which covers certain information security-related principles. Existing researchers in the field of information security still grapple with the “knowing-and-doing” gap, where user information security knowledge/awareness sometimes does not result in safer behavioural practises.

Originality/value

– Zhang et al. (2009) suggest that understanding human behaviour is important when dealing with the problems caused by human errors. Harnesk and Lindstrom (2011) expressed a concern that existing research does not address the interlinked relationship between anticipated security behaviour and the enactment of security procedures. This study acknowledges Choi et al. (2008) contribution in their discussions on the “knowing-and-doing gap” suggests a link between awareness and actual behaviour that is confirmed by the findings of this study.
Investigating the possibility to use differentiated authentication based on risk profiling to secure online banking
Authors: Butler Martin , Butler Rika
Published: October 2015

Purpose

– The purpose of this paper was to determine factors that could be used to create different authentication requirements for diverse online banking customers based on their risk profile. Online security remains a challenge to ensure safe transacting on the Internet. User authentication, a human-centric process, is regarded as the basis of computer security and hence secure access to online banking services. The increased use of technology to enforce additional actions has the ability to improve the quality of authentication and hence online security, but often at the expense of usability. The objective of this study was to determine factors that could be used to create different authentication requirements for diverse online banking customers based on their risk profile.

Design/methodology/approach

– A web-based survey was designed to determine online consumers’ competence resecure online behaviour, and this was used to quantify the online behaviour as more or less secure. The browsers used by consumers as well as their demographical data were correlated with the security profile of respondents to test for any significant variance in practice that could inform differentiated authentication.

Findings

– A statistical difference between behaviours based on some of the dependant variables was evident from the analysis. Based on the results, a case could be made to have different authentication methods for online banking customers based on both their browser selected (before individual identification) as well as demographical data (after identification) to ensure a safer online environment.

Originality/value

– The research can be used by the financial services sector to improve online security, where required, without necessarily reducing usability for more “security inclined” customers.
Effect of folic acid supplementation on risk of new‐onset diabetes in adults with hypertension in China: Findings from the China Stroke Primary Prevention Trial (CSPPT)
Authors: Qin Xianhui , Li Jianping , Zhang Yan , Chen Dafang , Wang Binyan , He Mingli , Fu Jia , Tang Genfu , Cai Yefeng , Shi Xiuli , Xu Xin , Hou Fan Fan , Wang Xiaobin , Huo Yong
Published: October 2015

Background

The aim of the present post hoc analysis of the China Stroke Primary Prevention Trial (CSPPT) was to evaluate the effect of folic acid supplementation on the risk of new‐onset diabetes in hypertensive adults in China.

Methods

In all, 20 702 hypertensive adults with no history of stroke and/or myocardial infarction (MI) were randomly assigned to receive double‐blind daily treatment with tablets containing either: (i) 10 mg enalapril and 0.8 mg folic acid (n = 10 348); or (ii) 10 mg enalapril alone (n = 10 354). New‐onset diabetes was defined as either self‐reported physician‐diagnosed diabetes or the use of glucose‐lowering drugs during the follow‐up period of the CSPPT.

Results

Over a median treatment duration of 4.5 years, new‐onset diabetes occurred in 198 (2.0%) and 214 (2.1%) subjects in the enalapril–folic acid and enalapril groups, respectively (hazard ratio [HR] 0.92; 95% confidence interval [CI] 0.76–1.12). Similar results were observed when analyses were limited to subjects with baseline fasting glucose (FG) <7.0 mmol/L (HR 0.85; 95% CI 0.62–1.14). Furthermore, there was no significant group difference in: (i) the risk of new‐onset FG ≥7.0 mmol/L (defined as FG <7.0 at baseline and ≥7.0 mmol/L at the last visit; relative risk [RR] 1.07; 95% CI 0.96–1.20); or (ii) the composite of new‐onset diabetes or new‐onset FG ≥7.0 mmol/L (RR = 1.06; 95% CI 0.95–1.19).

Conclusions

Among adults with hypertension with no history of stroke and/or MI in China, folic acid supplementation had no significant effect on the risk of new‐onset diabetes.
Optimizing sampling approaches along ecological gradients
Authors: Schweiger Andreas H. , Irl Severin D. H. , Steinbauer Manuel J. , Dengler Jürgen , Beierkuhnlein Carl
Published: October 2015

Natural scientists and especially ecologists use manipulative experiments or field observations along gradients to differentiate patterns driven by processes from those caused by random noise. A well‐conceived sampling design is essential for identifying, analysing and reporting underlying patterns in a statistically solid and reproducible manner, given the normal restrictions in labour, time and money. However, a technical guideline about an adequate sampling design to maximize prediction success under restricted resources is lacking. This study aims at developing such a solid and reproducible guideline for sampling along gradients in all fields of ecology and science in general.

We conducted simulations with artificial data for five common response types known in ecology, each represented by a simple function (no response, linear, exponential, symmetric unimodal and asymmetric unimodal). In the simulations, we accounted for different levels of random and systematic error, the two sources of noise in ecological data. We quantified prediction success for varying total sample size, number of locations sampled along a spatial/temporal gradient and number of replicates per sampled location.

The number of replicates becomes more important with increasing random error, whereas replicates become less relevant for a systematic error bigger than 20% of total variation. Thus, if high levels of systematic error are indicated or expected (e.g. in field studies with spatial autocorrelation, unaccountable additional environmental drivers or population clustering), continuous sampling with little to no replication is recommended. In contrast, sampling designs with replications are recommended in studies that can control for systematic errors. In a setting that is characteristic for ecological experiments and field studies strictly controlling for undeterminable systematic error (random error ≥10% and systematic error ≤10% of total variation), prediction success was best for an intermediate number of sampled locations along the gradient (10–15) and a low number of replicates per location (3).

Our findings from reproducible, statistical simulations will help design appropriate and efficient sampling approaches and avoid erroneous conclusions based on studies with flawed sampling design, which is currently one of the main targets of public criticism against science.
NecroX‐5 suppresses IgE/Ag‐stimulated anaphylaxis and mast cell activation by regulating the SHP‐1‐Syk signaling module
Authors: Li X. , Kwon O. , Kim D. Y. , Taketomi Y. , Murakami M. , Chang H. W.
Published: October 2015

Background

IgE/Ag‐stimulated mast cells release various pro‐allergic inflammatory mediators, including histamine, eicosanoids, and pro‐inflammatory cytokines. NecroX‐5, a cell permeable necrosis inhibitor, showed cytoprotective effects in both in vitro and in vivo models. However, the anti‐allergic effect of NecroX‐5 has not yet been investigated. The aims of this study were to evaluate the anti‐allergic activity of NecroX‐5 in vivo and to investigate the underlying mechanism in vitro.

Methods

The anti‐allergic activity of NecroX‐5 was evaluated in vitro using bone marrow‐derived mast cells (BMMCs) and IgE receptor‐bearing RBL‐2H3 or KU812 cells and in vivo using a mouse model of passive anaphylaxis. The levels of histamine, eicosanoids (PGD2 and LTC4), tumor necrosis factor‐α (TNF‐α), and interleukin‐6 (IL‐6) were measured using enzyme immunoassay kits. The mechanism underlying the action of NecroX‐5 was investigated using immunoblotting, immunoprecipitation, and gene knockdown techniques.

Results

NecroX‐5 markedly inhibited mast cell degranulation and the synthesis of eicosanoids, TNF‐α, and IL‐6 by suppressing the activation of Syk, LAT, phospholipase Cγ1, MAP kinases, the Akt/NF‐κB pathway, and intracellular Ca2+ mobilization via the activation of phosphatase SHP‐1. Oral administration of NecroX‐5 effectively suppressed mast cell‐dependent passive cutaneous and systemic anaphylactic reactions in a dose‐dependent manner.

Conclusions

NecroX‐5 might be a potential candidate for the development of a novel anti‐allergic agent that suppresses IgE‐dependent mast cells signaling.
Validating the WHO Maternal Near Miss Tool in a high‐income country
Authors: Witteveen Tom , de Koning Ilona , Bezstarosti Hans , van den Akker Thomas , van Roosmalen Jos , Bloemenkamp Kitty W.
Published: October 2015

Introduction

This study was performed to assess the applicability of the WHO Maternal Near Miss Tool (MNM Tool) and the organ dysfunction criteria in a high‐income country.

Material and methods

The MNM tool was applied to 2552 women who died of pregnancy‐related causes or sustained severe acute maternal morbidity between August 2004 and August 2006 in one of the 98 hospitals with a maternity unit in the Netherlands. Fourteen (0.6%) cases had insufficient data for application. Each case was assessed according to the three main “MNM categories” specified in the MNM tool and their subcategory criteria: five disease‐, four intervention‐ and seven organ dysfunction‐based criteria. Potentially life‐threatening conditions (disease‐based inclusions) and life‐threatening cases (organ dysfunction‐based inclusions) were differentiated according to WHO methodology. Outcomes were incidence of all (sub)categories and case‐fatality rates.

Results

Of the 2538 cases, 2308 (90.9%) women fulfilled disease‐based, 2116 (83.4%) intervention‐based and 1024 (40.3%) organ dysfunction‐based criteria. Maternal death occurred in 48 women, of whom 23 (47.9%) fulfilled disease‐based, 33 (68.8%) intervention‐based and 31 (64.6%) organ dysfunction‐based criteria. Case‐fatality rates were 23/2308 (1.0%) for cases fulfilling the disease‐based criteria, 33/2116 (1.6%) for intervention‐based criteria and 31/1024 (3.0%) for women fulfilling the organ dysfunction‐based criteria.

Conclusions

In the Netherlands, where advanced laboratory and clinical monitoring are available, organ dysfunction‐based criteria of the MNM tool failed to identify nearly two‐thirds of sustained severe acute maternal morbidity cases and more than one‐third of maternal deaths. Disease‐based criteria remain important, and using only organ dysfunction‐based criteria would lead to underestimating severe acute maternal morbidity.
Maternal overweight and sexual function in pregnancy
Authors: Ribeiro Meireluci C. , Nakamura Mary U. , Torloni Maria R. , Scanavino Marco de T. , Mancini Pedro E. , Forte Bruna M.B. , Mattar Rosiane
Published: October 2015

Introduction

Obesity and overweight are increasing worldwide and may compromise female sexual function. Our aim was to compare the sexual function of normal and overweight women in pregnancy.

Material and methods

A cross‐sectional study involving 223 pregnant women: 105 overweight [pre‐pregnancy body mass index (BMI) ≥25.0 kg/m2] and 118 normal weight (BMI 18.5–24.9 kg/m2), in the 2nd and 3rd trimester of pregnancy. These women were managed at an antenatal clinic of a public university hospital in São Paulo, Brazil, between 2011 and 2014. The Female Sexual Function Index (FSFI) was used. The characteristics of normal and overweight women were compared using two‐tailed Student's t‐ or chi‐squared tests. Differences in mean FSFI scores were assessed using the Kruskal–Wallis test. Pearson′s correlation coefficient was used to assess the correlation between pre‐pregnancy BMI and FSFI scores.

Results

In the 2nd trimester, mean total FSFI scores were similar in overweight (n = 51) compared to normal weight (n = 67) women (21.9 ± 9.8 vs. 21.7 ± 10.4, p = 1.000). In the 3rd trimester, overweight women (n = 54) had significantly lower total FSFI scores than normal weight women (n = 51; 19.1 ± 10.3 vs. 24.5 ± 9.7, p = 0.0004). In the 3rd trimester, overweight women also had significantly lower mean scores in desire, arousal, lubrication, orgasm and dyspareunia domains. We found an inverse correlation between pre‐pregnancy BMI and mean 3rd trimester total FSFI scores (r = −0.212, p = 0.030), desire (r = −0.216, p = 0.027) and orgasm (r = –0.222, p = 0.023).

Conclusion

Overweight women in the 3rd trimester of pregnancy had poorer sexual function compared with normal weight women.
THE MUDDLING CROWN: VIA RAIL AND THE FEDERAL GOVERNMENT
Authors: BIRD Malcolm G.
Published: October 2015

This article is an analysis of VIA Rail and its relationship with the federal government. Canada's publicly‐owned intercity passenger rail service is in a state of slow and steady decline, best illustrated by its small and falling user rates, and despite receiving significant subsidies, the federal government is indifferent to the needs of this transportation provider. Unlike other Canadian state‐owned enterprises, or Crown corporations, VIA Rail has been neither privatized nor modernized and, instead, is languishing as a publicly‐owned firm. While the current Conservative government of Stephen Harper favors a smaller role for the state, and it has both set about modernizing and eliminating other Crowns, it has not followed such a course with VIA Rail. Drawing on John Kingdon's (1984) multiple streams model to outline the empirical data as well as to illustrate how this firm interacts with its political superior, it will argue that the indifference towards this firm is due to both the specific characteristics of VIA Rail and the highly centralized decision‐making structure of Canada's Westminster Parliamentary system. Unless the federal government decides to implement fundamental organizational and governance changes at this firm, Canadians will continue to be served by a marginal rail service provider.
YES, NO, MAYBE: THE AMBIGUOUS RELATIONSHIPS BETWEEN STATE‐OWNED ENTERPRISES AND THE STATE
Authors: RENTSCH Carole , FINGER Matthias
Published: October 2015

Liberalization and the introduction of sector‐specific regulators has caused the position of State‐owned enterprises (SOEs) of network industries to change not only within national economies, but also vis‐à‐vis their respective States. In response, many SOEs are pursuing ambiguous strategies, simultaneously seeking autonomy and State protection. In turn, States, particularly in their roles as owners and regulators, have to rethink their relationships with SOEs. In French, German, and Swiss cases, both States and SOEs have motives to simultaneously maintain a close (‘yes’) and a distant (‘no’) relationship with one another. SOEs favour a close relationship to secure subsidization for the provision of public services, reduce financial risks, and build trust within collaboration. However, a distant relationship is more suitable for entrepreneurial autonomy and getting rid of the universal service obligation. From the State's perspective, a close relationship is desirable to ensure the stable provision of universal services, control politically and strategically important sectors and critical infrastructures, implement policy objectives, meet geopolitical objectives, and receive dividends as return on investment. A distant relationship is required to avoid bearing risk and to ensure freedom in regulating the public sector.
GOUVERNANCES PUBLIQUES ET ENTREPRISES PUBLIQUES DANS LES ÉCONOMIES DE RENTE
Authors: AHMED ZAID‐CHERTOUK Malika , BANCE Philippe
Published: October 2015

RESUME

Dans une économie de rente, les réformes économiques restent purement formelles et sont incapables de permettre à l'investissement national et international de se déployer. Elles ne permettent pas aux pays concernés de sortir de l'ordre social basé sur le gisement de la rente et la faible ouverture du système politico‐économique à la compétition. Sans perspective de croissance économique durable et de création d'emplois autres que ceux subventionnés par l'Etat, ce système fermé à la compétition porte en lui les germes de son dépassement : il ne peut répondre durablement à la demande sociale de changement et ne peut faire face aux difficultés croissantes de financement de la stabilité sociale.

Dans ce contexte, notre contribution se propose d'étudier les entreprises publiques évoluant dans une économie de rente et d'identifier les mécanismes permettant d'allouer les ressources de la rente au mieux de l'intérêt général. L'analyse amène dès lors à préciser comment repenser l'intérêt général national dans une économie de rente pour une meilleure prise en compte des besoins de développement durable. Comment reformuler les missions assignées aux entreprises publiques pour leur permettre d'internaliser au mieux cet intérêt général ? Quels nouveaux modes de gouvernance mettre en œuvre pour contribuer à la réalisation de ces objectifs ?

Mots clés : entreprises publiques, économie de rente, réformes économiques, gouvernances publiques, allocation de ressources, intérêt général.
TOWARDS CITIZEN ACCOUNTABILITY OF LOCAL PUBLIC ENTERPRISES
Authors: GREILING Dorothea , GRÜB Birgit
Published: October 2015

Since the liberalization of markets for public service provision within the nineties, the pressure on public sector entities to demonstrate their performance in financial and nonfinancial terms has increased. Compared to the private sector accountability expectations and obligations are higher for public enterprises due to public ownership and the specific public mission objectives. While there is a vast body of literature on public accountability in general, a research gap exists when it comes to the linkage of citizen accountability to the sustainability reporting practices of public enterprises. The paper analyses existing studies and adds a documentary analysis regarding sustainability reporting in German and Austrian public utilities.