bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
Authors: Krupa Paweł , Mozolewska Magdalena A. , Wiśniewska Marta , Yin Yanping , He Yi , Sieradzan Adam K. , Ganzynkowicz Robert , Lipska Agnieszka G. , Karczyńska Agnieszka , Ślusarz Magdalena , Ślusarz Rafał , Giełdoń Artur , Czaplewski Cezary , Jagieła Dawid , Zaborowski Bartłomiej , Scheraga Harold A. , Liwo Adam
Published: July 2016

Summary: Participating as the Cornell-Gdansk group, we have used our physics-based coarse-grained UNited RESidue (UNRES) force field to predict protein structure in the 11th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP11). Our methodology involved extensive multiplexed replica exchange simulations of the target proteins with a recently improved UNRES force field to provide better reproductions of the local structures of polypeptide chains. All simulations were started from fully extended polypeptide chains, and no external information was included in the simulation process except for weak restraints on secondary structure to enable us to finish each prediction within the allowed 3-week time window. Because of simplified UNRES representation of polypeptide chains, use of enhanced sampling methods, code optimization and parallelization and sufficient computational resources, we were able to treat, for the first time, all 55 human prediction targets with sizes from 44 to 595 amino acid residues, the average size being 251 residues. Complete structures of six single-domain proteins were predicted accurately, with the highest accuracy being attained for the T0769, for which the CαRMSD was 3.8 Å for 97 residues of the experimental structure. Correct structures were also predicted for 13 domains of multi-domain proteins with accuracy comparable to that of the best template-based modeling methods. With further improvements of the UNRES force field that are now underway, our physics-based coarse-grained approach to protein-structure prediction will eventually reach global prediction capacity and, consequently, reliability in simulating protein structure and dynamics that are important in biochemical processes.

Availability and Implementation: Freely available on the web at http://www.unres.pl/ .

Contact:  has5@cornell.edu
Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data
Authors: Devailly Guillaume , Mantsoki Anna , Joshi Anagha
Published: July 2016

Summary: Better protocols and decreasing costs have made high-throughput sequencing experiments now accessible even to small experimental laboratories. However, comparing one or few experiments generated by an individual lab to the vast amount of relevant data freely available in the public domain might be limited due to lack of bioinformatics expertise. Though several tools, including genome browsers, allow such comparison at a single gene level, they do not provide a genome-wide view. We developed Heat*seq, a web-tool that allows genome scale comparison of high throughput experiments chromatin immuno-precipitation followed by sequencing, RNA-sequencing and Cap Analysis of Gene Expression) provided by a user, to the data in the public domain. Heat*seq currently contains over 12 000 experiments across diverse tissues and cell types in human, mouse and drosophila. Heat*seq displays interactive correlation heatmaps, with an ability to dynamically subset datasets to contextualize user experiments. High quality figures and tables are produced and can be downloaded in multiple formats.

Availability and Implementation: Web application: http://www.heatstarseq.roslin.ed.ac.uk/ . Source code: https://github.com/gdevailly .

Contact:  Guillaume.Devailly@roslin.ed.ac.uk or Anagha.Joshi@roslin.ed.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
w4CSeq: software and web application to analyze 4C-seq data
Authors: Cai Mingyang , Gao Fan , Lu Wange , Wang Kai
Published: July 2016

Summary: Circularized Chromosome Conformation Capture followed by deep sequencing (4C-Seq) is a powerful technique to identify genome-wide partners interacting with a pre-specified genomic locus. Here, we present a computational and statistical approach to analyze 4C-Seq data generated from both enzyme digestion and sonication fragmentation-based methods. We implemented a command line software tool and a web interface called w4CSeq, which takes in the raw 4C sequencing data (FASTQ files) as input, performs automated statistical analysis and presents results in a user-friendly manner. Besides providing users with the list of candidate interacting sites/regions, w4CSeq generates figures showing genome-wide distribution of interacting regions, and sketches the enrichment of key features such as TSSs, TTSs, CpG sites and DNA replication timing around 4C sites.

Availability and Implementation: Users can establish their own web server by downloading source codes at https://github.com/WGLab/w4CSeq . Additionally, a demo web server is available at http://w4cseq.wglab.org .

Contact:  kaiwang@usc.edu or wangelu@usc.edu

Supplementary information : Supplementary data are available at Bioinformatics online.
Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees
Authors: Yamada Kazunori D. , Tomii Kentaro , Katoh Kazutaka
Published: July 2016

Motivation: Large multiple sequence alignments (MSAs), consisting of thousands of sequences, are becoming more and more common, due to advances in sequencing technologies. The MAFFT MSA program has several options for building large MSAs, but their performances have not been sufficiently assessed yet, because realistic benchmarking of large MSAs has been difficult. Recently, such assessments have been made possible through the HomFam and ContTest benchmark protein datasets. Along with the development of these datasets, an interesting theory was proposed: chained guide trees increase the accuracy of MSAs of structurally conserved regions. This theory challenges the basis of progressive alignment methods and needs to be examined by being compared with other known methods including computationally intensive ones.

Results: We used HomFam, ContTest and OXFam (an extended version of OXBench) to evaluate several methods enabled in MAFFT: (1) a progressive method with approximate guide trees, (2) a progressive method with chained guide trees, (3) a combination of an iterative refinement method and a progressive method and (4) a less approximate progressive method that uses a rigorous guide tree and consistency score. Other programs, Clustal Omega and UPP, available for large MSAs, were also included into the comparison. The effect of method 2 (chained guide trees) was positive in ContTest but negative in HomFam and OXFam. Methods 3 and 4 increased the benchmark scores more consistently than method 2 for the three datasets, suggesting that they are safer to use.

Availability and Implementation:  http://mafft.cbrc.jp/alignment/software/

Contact:  katoh@ifrec.osaka-u.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
A calibration method for realistic neutron dosimetry in radiobiological experiments assisted by MCNP simulation
Authors: Shahmohammadi Beni Mehrdad , Krstic Dragana , Nikezic Dragoslav , Yu Kwan Ngok
Published: July 2016

Many studies on biological effects of neutrons involve dose responses of neutrons, which rely on accurately determined absorbed doses in the irradiated cells or living organisms. Absorbed doses are difficult to measure, and are commonly surrogated with doses measured using separate detectors. The present work describes the determination of doses absorbed in the cell layer underneath a medium column ( DA ) and the doses absorbed in an ionization chamber ( DE ) from neutrons through computer simulations using the MCNP-5 code, and the subsequent determination of the conversion coefficients R (=  DA / DE ). It was found that R in general decreased with increase in the medium thickness, which was due to elastic and inelastic scattering. For 2-MeV neutrons, conspicuous bulges in R values were observed at medium thicknesses of about 500, 1500, 2500 and 4000 μm, and these were attributed to carbon, oxygen and nitrogen nuclei, and were reflections of spikes in neutron interaction cross sections with these nuclei. For 0.1-MeV neutrons, no conspicuous bulges in R were observed (except one at ~2000 μm that was due to photon interactions), which was explained by the absence of prominent spikes in the interaction cross-sections with these nuclei for neutron energies <0.1 MeV. The ratio R could be increased by ~50% for small medium thickness if the incident neutron energy was reduced from 2 MeV to 0.1 MeV. As such, the absorbed doses in cells ( DA ) would vary with the incident neutron energies, even when the absorbed doses shown on the detector were the same.
The Niche for Escherichia coli Sequence Type 131 Among Veterans: Urinary Tract Abnormalities and Long-Term Care Facilities
Authors: Drekonja Dimitri M. , Kuskowski Michael A. , Anway Ruth , Johnston Brian D. , Johnson James R.
Published: July 2016

Background.  Antimicrobial resistance among Escherichia coli is increasing, driven largely by the global emergence of sequence type 131 (ST131). However, the clinical significance of ST131 status is unknown. Among veterans, we assessed whether ST131 causes more severe, persistent, or recurrence-prone infections than non-ST131 E. coli.

Methods.  Isolates were assessed by polymerase chain reaction for membership in ST131 and relevant subclones thereof (H30R and H30Rx) and by broth microdilution for susceptibility to 11 antibiotics. Clinical and epidemiological data were systematically abstracted from the medical record. Between-group comparisons were made using t tests and Fisher's exact test.

Results.  Of the 311 unique E. coli isolates, 61 (19.6%) represented ST131. Of these, most (51 of 61, 83.6%) represented the H30R subclone; only 5 of 51 (9.8%) represented H30Rx. Relative to non-ST131 and non-H30R isolates, neither ST131 nor H30R were associated with more severe disease, worse clinical outcomes, or more robust hosts. Instead, both were more likely to be isolated from patients without manifestations of infection (for ST131, 36.1% vs 21.2% [P = .02]; for H30R, 39% vs 21% [P = .008]) and who had prior healthcare contact or long-term care facility (LTCF) exposure (for ST131, 33% vs 14% [P = .002]; for H30R, 37% vs 14% [P < .001]). Despite a greater likelihood of discordant initial therapy, outcomes did not differ between ST131 and H30R isolates vs other E. coli isolates.

Conclusions.  Among veterans, ST131 and its H30R subclone were associated with LTCF-exposed hosts but not with worse outcomes.
Linkage to Care, Early Infant Diagnosis, and Perinatal Transmission Among Infants Born to HIV-Infected Nigerian Mothers: Evidence From the Healthy Beginning Initiative
Authors: Pharr Jennifer R. , Obiefune Michael C. , Ezeanolue Chinenye O. , Osuji Alice , Ogidi Amaka G. , Gbadamosi Semiu , Patel Dina , Iwelunmor Juliet , Yang Wei , Ogedegbe Gbenga , Ehiri John E. , Sam-Agudu Nadia A. , Ezeanolue Echezona E.
Published: July 2016

Background:

In 2014, Nigeria accounted for 33% of all new childhood HIV infections that occurred among the 22 Global Plan priority countries where 80% of HIV-infected women reside. Even with a vertical HIV transmission rate of 27%, only 6% of infants born to HIV-infected women in Nigeria receive early infant diagnosis (EID). This article reports rates of antiretroviral prophylaxis, EID, and mother-to-child transmission in a congregation-based Healthy Beginning Initiative (HBI) designed to increase HIV testing among pregnant women in southeast Nigeria.

Methods:

This is a nested cohort study of HIV-exposed infants (HEI) within the HBI trial originally designed as a 2-arm cluster randomized trial. HIV-infected mothers and infants were followed between January 2013 and August 2014.

Results:

Across both arms of the study, 72 HIV-infected women delivered 69 live infants (1 set of twins) and 4 had miscarriages. Of the 69 live-born HEI, HIV status was known for 71% (49/69), 16% (11/69) died before sample collection, and 13% (9/69) were lost to follow-up. Complete information was available for 84% of HEI (58/69), of which 64% (37/58) received antiretroviral prophylaxis. Among the 49 infants tested for HIV, 88% (43/49) received EID within 2 months and 12% (6/49) received antibody testing after 18 months. The mother-to-child transmission rate was 8.2% (4/49).

Conclusions:

EID was higher and HIV transmission rate was lower among the HBI participants compared to reported rates in 2014. However, further progress is needed to achieve goals of elimination of infant HIV infection.
A Protocol for a Cluster Randomized Trial on the Effect of a “feeding buddy” Program on adherence to the Prevention of Mother-To-Child-Transmission Guidelines in a Rural Area of KwaZulu-Natal, South Africa
Authors: Reimers Penelope , Israel-Ballard Kiersten , Spies Lenore , Tanser Frank , Thior Ibou , Scott Gordon W. , Coutsoudis Anna
Published: July 2016

Background:

The uptake of prevention of mother-to-child-transmission (PMTCT) services has improved in South Africa but challenges remain, including adherence to the World Health Organization's (WHO) PMTCT recommendations of exclusive breastfeeding (EBF), taking antiretroviral medication (ARV); testing for early infant diagnosis; and reducing stigma. Women who practice EBF for the first 6 months are less likely to transmit HIV to their infants, yet only 7% of women EBF for 6 months in South Africa. Adherence to these recommendations remains challenging because of difficulties relating to disclosure and stigma. To address this challenge, the feeding buddy concept was developed based on studies where ARV buddies have proved effective in providing support for women living with HIV. Buddies have demonstrated a positive effect on providing emotional and social support to adhere to PMTCT guidelines.

Methods:

A cluster randomized controlled trial was conducted in 16 selected randomly assigned clinics in uMhlathuze and uMlalazi districts of KwaZulu Natal, South Africa. HIV-positive pregnant women (n = 625) who intended to breastfeed were enrolled at 8 control clinics and 8 intervention clinics. The clinics were stratified on the basis of urban/rural/periurban locale and then randomly allocated to either intervention or control. In the intervention clinics, the mother chose a feeding buddy to be enrolled alongside her. Quantitative interviews with mothers and their chosen buddies took place at enrollment during pregnancy and at routine postdelivery visits at day 3 and weeks 6, 14 and 22. Women in the control clinics were followed using the same evaluation schedule. The trial evaluated the effect of a voluntary PMTCT feeding buddy program on HIV-infected women's adherence to PMTCT recommendations and stigma reduction. The proportion of women exclusively feeding at 5.5 months postpartum was the primary end-point of the trial. In-depth interviews were conducted among a convenience sample of PMTCT counselors, community caregivers, mothers, and buddies from intervention clinics and control clinics to document their overall experiences.

Discussion:

The information collected in this study could be used to guide recommendations on how to build upon the current South Africa. PMTCT “buddy” strategy and to improve safe infant feeding. The information would be applicable to many other similar resource poor settings with poor social support structures.
Identifying and Prioritizing Implementation Barriers, Gaps, and Strategies Through the Nigeria Implementation Science Alliance: Getting to Zero in the Prevention of Mother-to-Child Transmission of HIV
Authors: Ezeanolue Echezona E. , Powell Byron J. , Patel Dina , Olutola Ayodotun , Obiefune Michael , Dakum Patrick , Okonkwo Prosper , Gobir Bola , Akinmurele Timothy , Nwandu Anthea , Torpey Kwasi , Oyeledum Bolanle , Aina Muyiwa , Eyo Andy , Oleribe Obinna , Ibanga Ikoedem , Oko John , Anyaike Chukwuma , Idoko John , Aliyu Muktar H. , Sturke Rachel , Watts Heather , Siberry George ,   the Nigeria Implementation Science Alliance
Published: July 2016

Background:

In 2013, Nigeria accounted for 15% of the 1.3 million pregnant women living with HIV in sub-Saharan Africa and 26% of new infections among children worldwide. Despite this, less than 20% of pregnant women in Nigeria received an HIV test during pregnancy, and only 23% of HIV-infected pregnant women received appropriate intervention following HIV diagnosis. This article reports findings from 2 structured group exercises conducted at the first Nigeria Implementation Science Alliance Conference to identify (1) barriers and research gaps related to prevention of mother-to-child transmission (PMTCT) and (2) potential strategies and interventions that could address PMTCT challenges.

Methods:

Two 1-hour structured group exercises were conducted with 10 groups of 14–15 individuals (n = 145), who were asked to brainstorm barriers and strategies and to rank their top 3 in each category. Data analysis eliminated duplicate responses and categorized each of the priorities along the HIV care continuum: HIV diagnosis, linkage to care, or retention in care.

Results:

Participating stakeholders identified 20 unique barriers and research gaps related to PMTCT across the HIV continuum. Twenty-five unique interventions and implementation strategies were identified. Similar to the barriers and research gaps, these interventions and strategies were distributed across the HIV care continuum.

Conclusions:

The barriers and strategies identified in this study represent important pathways to progress addressing MTCT. The deliberate involvement of state and federal policy makers, program implementers, and researchers helps ensure that they are relevant and actionable.
Vitamin D, reactive oxygen species and calcium signalling in ageing and disease
Authors: Berridge Michael J.
Published: July 2016

Vitamin D is a hormone that maintains healthy cells. It functions by regulating the low resting levels of cell signalling components such as Ca
2+
and reactive oxygen species (ROS). Its role in maintaining phenotypic stability of these signalling pathways depends on the ability of vitamin D to control the expression of those components that act to reduce the levels of both Ca
2+
and ROS. This regulatory role of vitamin D is supported by both Klotho and Nrf2. A decline in the vitamin D/Klotho/Nrf2 regulatory network may enhance the ageing process, and this is well illustrated by the age-related decline in cognition in rats that can be reversed by administering vitamin D. A deficiency in vitamin D has also been linked to two of the major diseases in man: heart disease and Alzheimer's disease (AD). In cardiac cells, this deficiency alters the Ca
2+
transients to activate the gene transcriptional events leading to cardiac hypertrophy and the failing heart. In the case of AD, it is argued that vitamin D deficiency results in the Ca
2+
landscape that initiates amyloid formation, which then elevates the resting level of Ca
2+
to drive the memory loss that progresses to neuronal cell death and dementia.

This article is part of the themed issue ‘Evolution brings Ca
2+
and ATP together to control life and death’.
NGMASTER:
in silico multi-antigen sequence typing for Neisseria gonorrhoeae
Authors: Kwong Jason C. , Gonçalves da Silva Anders , Dyet Kristin , Williamson Deborah A. , Stinear Timothy P. , Howden Benjamin P. , Seemann Torsten
Published: July 2016

Whole-genome sequencing (WGS) provides the highest resolution analysis for comparison of bacterial isolates in public health microbiology. However, although increasingly being used routinely for some pathogens such as Listeria monocytogenes and Salmonella enterica, the use of WGS is still limited for other organisms, such as Neisseria gonorrhoeae. Multi-antigen sequence typing (NG-MAST) is the most widely performed typing method for epidemiological surveillance of gonorrhoea. Here, we present NGMASTER, a command-line software tool for performing in silico NG-MAST on assembled genome data. NGMASTER rapidly and accurately determined the NG-MAST of 630 assembled genomes, facilitating comparisons between WGS and previously published gonorrhoea epidemiological studies. The source code and user documentation are available at https://github.com/MDU-PHL/ngmaster.
Third-party coordination in conflict resolution: evidence from Nepal and the Philippines
Authors: Bhattarai Prakash
Published: July 2016

Purpose

This study aims to explore the conditions that lead to the occurrence of third-party interveners’ coordination in conflict resolution efforts.

Design/methodology/approach

The studied theme is elaborated by means of an analysis of two case studies: the Maoist armed conflict of Nepal and the Moro conflict of the Philippines. Importantly, this study solicits the views of third-party practitioners and other relevant stakeholders in the field and attempts to demonstrate how they perceive key issues in third-party coordination.

Findings

Third-party coordination is a contingent process, with varying needs and relevance in different phases and types of conflict. The escalation of violence, issues of international concern such as human rights and the homogeneity of interveners are other core elements that have often played a key role in third-party coordination.

Research limitations/implications

In the existing literature, there are no such indicator-based explanations regarding the occurrence of third-party coordination; thus, the findings of this research on this particular theme are well-developed and better conceptualized than what has been discussed in the literature to date.

Practical implications

The analysis undertaken in this study can contribute to the design of better policies and strategies for third-party coordination.

Originality/value

This study is based on in-depth interviews and interactions with a diverse range of third-party practitioners and other stakeholders working in real-world conflicts, who have perhaps the best understanding of various dimensions of third-party coordination. No previous research has been conducted on this particular theme by incorporating direct interaction with a wide range of interveners from two distinct conflict contexts.
How emerging markets firms will become global leaders
Authors: Grosse Robert
Published: July 2016

Purpose

– Over time the countries characterized as “emerging” change, and some of the companies from these countries become world leaders even as many of those from traditional economic powers fade. There is nothing guaranteed about success of companies from emerging markets (EMs), other than the fact that some of the firms that do survive will be among the success stories of the future. The purpose of this paper is to explore two questions: what enables companies from EMs to compete with existing firms? Is there a conceptual structure that is best for analyzing these firms and their strategies?

Design/methodology/approach

– This paper discusses the strengths of EM multinational enterprises (MNEs) from the perspective of Dunning’s eclectic view, and gives four detailed examples of companies from this perspective.

Findings

– It is suggested that while the eclectic view offers excellent insight into EM MNEs, an analysis of their strategies and policy implications requires further perspective such as through the global value-added chain.

Research limitations/implications

– No single model will capture all of the important features of EM MNEs, but Dunning’s view and the global value-added chain are good tools.

Practical implications

– Hopefully, both research analysts and company managers will be able to utilize the view presented here to better manage/understand EM MNEs.

Originality/value

– This view demonstrates a mechanism for exploring key elements of EM MNEs and by moving to the global value-added chain additional, original perspective is gained.
Do public support services matter in the multilocation process in China?
Authors: Portero Borja , Puig Francisco
Published: July 2016

Purpose

– During the last decade the demand to comprehend the overarching success factors of the multilocation process in distant countries such as China has increased significantly. In this context, the purpose of this paper is to explore and understand the nature and scope of the collaboration between the public support services (PSS) in China and the Spanish enterprises which decided to be multilocated there.

Design/methodology/approach

– The present study examines the necessity of the PSS in China by employing a review of literature as well as both quantitative and qualitative surveys from 31 Spanish companies multilocated in China.

Findings

– The main conclusions highlight the fact that the PSS do not seem to have a big and homogenous influence on the multilocation process, although those companies with higher levels of commitment that have been operating in China for a longer time have used it more frequently.

Originality/value

– While other studies of multilocation have isolated the companies from their host environment, the aim of this paper is to evaluate the weak links between the PSS and companies in a culturally and psychically distant market. By providing an insight into the dynamics of how firms interact and collaborate with the PSS, this study contributes to guiding policy makers and managers in designing and implementing strategies to support enterprises in the multilocation process in China.
Observers versus agents
Authors: Ahn Dohyun , Shin Dong-Hee
Published: July 2016

Purpose

– The purpose of this paper is to explore whether distinctive modes (observation vs control) of presenting diverse content differentially influence users. To achieve this goal, The authors first conceptualize empathy as social cognition and discuss the possible psychological mechanisms for divergent associations between observation-based media (i.e. video media) and control-based media (i.e. game media).

Design/methodology/approach

– In total, 300 adults (150 females) participated in this study through an online survey.

Findings

– Time spent with video media (television and film) was positively associated with empathy, which in turn was associated with enhanced social connectedness. However, time spent on game media (video games, computer games, and smartphone games) was negatively associated with empathy, which in turn was associated with inferior social connectedness.

Originality/value

– While previous studies on the effects of media have focussed mainly on content, the present study focusses on the effects of mode. The mode-focussed approach presents evidence contradictory to the content-focussed approach.
Modelling volatility and forecasting of exchange rate of British pound sterling and Indian rupee
Authors: Gupta Sanjeev , Kashyap Sachin
Published: July 2016

Purpose

The paper aims to analyse the extent of volatility and generating forecasts of exchange rates of British pound and Indian rupees in US terms.

Design/methodology/approach

This study applies different combinations of GARCH and EGARCH models suggested in the Econometric literature to capture the extent of volatility. The forecast of exchange rates of British Pound and Indian Rupees in US terms are generated applying artificial neural network (ANN) technique using different combination of networks with hyperbolic tangent function at hidden and output stage of the model.

Findings

The presence of volatility depicts that there is noise and chaos in the forex market. Prediction of exchange rate of the respective currencies underscores that exchange rates will increase marginally in near future.

Practical Implications

The results proposed in this study will be benchmark for the hedgers, investors, bankers, practitioners and economists to foresee the exchange rate in the presence of volatility and design policies accordingly.

Originality/value

In literature, no study has applied ANN for forecasting exchange rate after measuring the extent of volatility. The present study is a unique contribution in the existing pool of literature to forecasts the concerned variable(s) after ascertaining the noise and chaos in the data by applying GARCH family models.
Replications hardly possible: reporting practice in top-tier marketing journals
Authors: Lehmann Sebastian , Bengart Paul
Published: July 2016

Purpose

The purpose of this paper is to highlight the role of replications for science, and in particular the knowledge development process.

Design/methodology/approach

Descriptive research on the disclosure of sample parameters which are needed for replication was conducted. The analysis includes 2,982 studies from four top-tier marketing journals.

Findings

Published parameters are insufficient for replication and, therefore, impede knowledge development.

Originality/value

The paper offers a unique data set for further investigation. In total, 2,982 studies from the defined journals (Journal of Consumer Research, Journal of Marketing, Journal of Marketing ResearchandMarketing Science) were analyzed. Hereby this paper enables insights into reporting practices of current marketing research and highlights the role of replication research in validating earlier research. It empirically shows, to the authors' best knowledge for the first time, that the insufficient reporting is one of the major reasons for the lack of replications.
The holographic service innovation in technological context
Authors: Khaksar Seyed Mohammad Sadegh , Khosla Rajiv , Chu Mei-Tai , Shahmehr Fatemeh S.
Published: July 2016

Purpose

The purpose of this paper is to propose a new approach that enables service innovation models to incorporate a holographic perspective into their innovation-centric business models. The essence of the holographic approach to service innovation might provide us with an innovative organization that is enclosed in its components; a knowledge-centric approach that adapts each person as a vital component of a whole; and the ability of value co-creation by each part of the organization in ways that benefit the organization as a whole.

Design/methodology/approach

This paper uses a narrative synthesis framework combining existing literature (by textual narrative technique) with expert opinion, based on search of Science-Direct and ProQuest academic databases.

Findings

A total of 114 top-cited and high relevant references were deeply reviewed. Nine principle dimensions were evolved from the final review to construct a comprehensive definition of service innovation. Then, the narrative synthesis helped us to bring forward a new approach to service innovation and applied it in the form of a conceptual model, as the literature was previously established on certain approaches. In the final stage, a comprehensive model of service innovation was designed to introduce the holographic approach to the existing literature.

Research limitations/implications

This paper reviewed top-cited and high relevant references published in English that were indexed in Science-Direct and ProQuest. The authors did not search any grey literature and other language publications, and hand-search any journals.

Practical implications

This research highlights how managers must consider service innovation as a whole.

Originality/value

This is the first critical review published in the peer-reviewed literature that explores the principle dimensions of service innovation and provide a new approach to the literature.
Determining bucket structures in pricing plans for private user cloud computing storage services
Authors: Gerpott Torsten J. , May Sebastian
Published: July 2016

Purpose

Providers of cloud computing storage services (CCSS) charge offers in several unit bundles for a lump sum per bundle. This non-linear pricing approach is known as a bucket-pricing plan (BPP). If a customer exploits the purchased bucket, he/she can opt for the next higher bucket or refrain from further CCSS use. CCSS suppliers are faced with an optimization problem concerning the number of buckets as well as their lower and upper storage volume boundaries. The purpose of this paper is to develop a model, which supports CCSS suppliers in deriving a BPP-structure and which maximizes their profit in varying market constellations.

Design/methodology/approach

The authors develop a multi-period model of tariff choice decisions of private customers of CCSS. The model is applied in Monte Carlo simulations to determine profit-maximal tariff structures as a function of different market characteristics such as median demand saturation, demand heterogeneity, average price per storage unit and bucket ceiling allocation (identical size of each bucket within the frame set by the lower and upper overall boundary, varying sizes of the buckets offered, so that the interval between two ceilings consecutively increases for subsequent buckets) and type of a customer’s utility function.

Findings

The simulation analysis suggests that demand heterogeneity and average price per unit are the most influential factors for CCSS tariff structure optimization. Price plans with more than two buckets tend to generate higher profits than simple schemes with two buckets only if demand heterogeneity is low and the average price per storage unit is high and/or median saturation level of customers is low.

Originality/value

Despite the popularity of BPP among providers of CCSS for consumers, there is a lack of scholarly modeling work on the profit implications of the number of buckets entailed in a scheme and the size/ceilings of the various buckets on offer. The model suggested in this paper is a first step toward narrowing this research gap.
Breaking through barriers: the impact of organizational culture on open government reform
Authors: Ruijer Erna H.J.M. , Huff Richard F.
Published: July 2016

Purpose

The purpose of this paper is to examine the impact of organizational culture on open government reforms by developing a theoretical framework bridging the theory and practice gap.

Design/methodology/approach

An exploratory qualitative study consisting of a document analysis and a case study was conducted.

Findings

An open organizational culture is a precursor to effective open government. A network strategy as a facilitator for developing an open culture was used in one US federal agency, breaking across boundaries within the organization, creating greater symmetrical horizontal and vertical openness.

Originality/value

Much of the focus in both theory and practice has been on the use of technology as a vehicle to increase government openness. This study argues that a movement toward openness is beyond the technical. Organizational culture is a key to openness and may need to be changed. A networks strategy may be one way to facilitate a transformation to a more open culture.
Socio-demographic portrait of Russian travelers
Authors: Kalabikhina Irina E. , Shishalov Dmitry
Published: July 2016

Purpose

Focuses on the social and demographic features of inbound and outbound Russian travelers, in particular, on target groups of travelers and the challenges they face in Russia.

Design/methodology/approach

Draws on analysis of Synovate Comcon Russian Target Group Index and TNS Marketing Index databases, Rosstat data, expert round table discussion with author participation and observation and interviews in tourist-related sites during 2014-2015.

Findings

The most important factors for domestic tourism are family status, employment, income and education. Demographic target groups for internal tourism in Russia include: low-income retired persons; groups of students; working qualified experts and family travelers. The most important factors affecting external travel are region of residence, the size of the city and income status. Political challenges (including the closure of Russians of destinations in Egypt and Turkey) tend to reinforce economic crisis and national currency depreciation. Nevertheless, forecasts of industry development predict a slow recovery over the next few years up to 2019.

Originality/value

Outlines the demographic and social target groups of inbound and outbound Russian travelers described in the context of new circumstances in Russia. This information could be used by practitioners to develop travel and tourist packages for Russian tourists.
Browsing by an invasive herbivore promotes development of plant and soil communities during primary succession
Authors: Bellingham Peter J. , Kardol Paul , Bonner Karen I. , Buxton Rowan P. , Morse Chris W. , Wardle David A.
Published: July 2016

Invasive herbivores can strongly affect ecosystems by reducing or removing native plant species, and early in primary successions they could have enduring consequences for plant community assembly and ecosystem functioning, although this has seldom been explored. Invasive brushtail possums (Trichosurus vulpecula) browse from ground levels to forest canopies in New Zealand, including on plant species common early in primary succession.

We used exclosures (fenced on the top as well as the sides) and corresponding control plots to study effects of brushtail possums on primary successions on bare landslide surfaces in the South Island of New Zealand. We then conducted repeated measurements of the plant community over 11 years and at the end also quantified soil abiotic and biotic properties.

Above‐ground, plant biomass increased from close to zero to > 1000 g dry mass m−2after 11 years in both exclosures and control plots, with significantly more biomass of the N2‐fixing treeCarmichaelia odoratain the controls. Brushtail possums reduced the biomass in the control plots of small‐stature grasses and sedges in the first 3 years. Plant species richness was greater in control than exclosure plots throughout the experiment.

Below‐ground, soil carbon and nitrogen concentrations and the biomass of all major soil microbial groups were significantly greater in the control than exclosure plots, although soil nematode abundances were not. Below‐ground effects could be attributed to the greater biomass ofCarmichaeliain control plots.

Synthesis. Our study shows that an invasive herbivore exerted strong effects on the rate and trajectory of primary succession by altering plant community assembly. Herbivore exclusion resulted in reduced biomass of a key N2‐fixing tree that drives forest development, with important below‐ground consequences. These results support a view that restoration of ecosystems needs to consider the consequences of altering plant community structure before removing invasive herbivores.
So close and yet so far away: long‐distance dispersal events govern bryophyte metacommunity reassembly
Authors: Barbé Marion , Fenton Nicole J. , Bergeron Yves
Published: July 2016

Metapopulation dynamics have been used to explain bryophyte dispersal patterns and they predict that population abundances vary with the spatial distribution of habitat and with species traits. However, results from stand and landscape studies are contradictory as both distance‐dependent and distance‐independent patterns have been found. These studies have typically included only a few species, which limits interspecies comparison. It is the time to investigate bryophyte dispersal at the metacommunity scale.

We studied bryophyte dispersal patterns in a system made up of burned matrices containing unburned residual forest patches. The importance of short‐ versus long‐distance dispersal was examined by comparing extant and propagule rain communities in residual forest patches of three fire sites using both species and life strategies.

Extant and propagule rain communities were distinct. Several propagule rain species, of all life strategies, did not originate from the closest extant community, suggesting that regional dispersal events are important, following the inverse isolation hypothesis.

Temporal, spatial and structural characteristics of the environment had a greater influence on dispersal than distance, which only influenced similarity patterns at the regional scale, highlighting the importance of propagule source attributes for the conservation of bryophyte metacommunities.

Synthesis. Long‐distance dispersal may be the rule and not the exception in bryophyte metacommunities. Therefore, bryophyte metacommunity dynamics depend on several dispersal scales, and residual forest patches can contribute both to local and regional diaspore clouds. Species’ environmental tolerance during establishment and their ability to produce copious amounts of spores may be more important filters in bryophyte metacommunity dynamics than dispersal distance.
VCP746, a novel A1 adenosine receptor biased agonist, reduces hypertrophy in a rat neonatal cardiac myocyte model
Authors: Chuo Chung H , Devine Shane M , Scammells Peter J , Krum Henry , Christopoulos Arthur , May Lauren T , White Paul J , Wang Bing H
Published: July 2016

VCP746 is a novel A1 adenosine receptor (A1AR) biased agonist previously shown to be cytoprotective with no effect on heart rate. The aim of this study was to investigate the potential anti‐hypertrophic effect of VCP746 in neonatal rat cardiac myocytes (NCM). NCM hypertrophy was stimulated with interleukin (IL)‐1β (10 ng/mL), tumour necrosis factor (TNF)‐α (10 ng/mL) or Ang II (100 nmol/L) and was assessed by 3H‐leucine incorporation assay. VCP746 significantly inhibited IL‐1β‐, TNF‐α‐ and Ang II‐stimulated NCM hypertrophy as determined by 3H‐leucine incorporation. The anti‐hypertrophic effect of VCP746 was also more potent than that of the prototypical A1AR agonist, N6‐cyclopentyladenosine (CPA). Further investigation with the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) cell viability assay showed that neither CPA nor VCP746 had any effect on cell viability, confirming that the reduction in 3H‐leucine incorporation mediated by CPA and VCP746 was not due to a reduction in cell viability. IL‐1β, TNF‐α and Ang II were also shown to increase the mRNA expression of hypertrophy biomarkers, ANP, β‐MHC and α‐SKA in NCM. Treatment with VCP746 at concentrations as low as 1 nmol/L suppressed mRNA expression of ANP, β‐MHC and α‐SKA stimulated by IL‐1β, TNF‐α or Ang II, demonstrating the broad mechanistic basis of the potent anti‐hypertrophic effect of VCP746. This study has shown that the novel A1AR agonist, VCP746, is able to attenuate cardiac myocyte hypertrophy. As such, VCP746 is potentially useful as a pharmacological agent in attenuating cardiac remodelling, especially in the post‐myocardial infarction setting, given its previously established cytoprotective properties.
The role of apelin in central cardiovascular regulation in rats with post‐infarct heart failure maintained on a normal fat or high fat diet
Authors: Czarzasta Katarzyna , Cudnoch‐Jedrzejewska Agnieszka , Szczepanska‐Sadowska Ewa , Fus Lukasz , Puchalska Liana , Gondek Agata , Dobruch Jakub , Gomolka Ryszard , Wrzesien Robert , Zera Tymoteusz , Gornicka Barbara , Kuch Marek
Published: July 2016

Based on the available literature, it can be assumed that in cases of post‐infarct heart failure (HF) and obesity, a significant change in the central regulation of the cardiovascular system takes place with, among others, the involvement of the apelinergic system. The main objective of the present study was to clarify the role of apelin‐13 in the central regulation of the cardiovascular system in Sprague Dawley rats withHFor sham operated (SO) and fed on a normal fat (NFD) or a high fat diet (HFD). The study was divided into two parts: Part I, hemodynamic studies; and PartII, biochemical and molecular studies. The animals were subjected to the following research procedures. Part I andII: feedingNFDorHFD; experimental induction ofHForSO; Part I: intracerebroventricular (ICV) infusion of the examined substances, monitoring of mean arterial blood pressure (MABP) and heart rate (HR); PartII: venous blood and tissue samples collected.ICVinfusion of apelin‐13 caused significantly higher changes in ΔMABPin theSO NFDgroup. No changes were noted in ΔHRin any of the studied groups. Apelin and apelin receptor (APJ)mRNAexpression in the brain and adipose tissues was higher in theHFrats.HFDcauses significant increase in expression of apelin andAPJ mRNAin the left ventricle. In conclusion,HFandHFDappear to play an important role in modifying the activity of the central apelinergic system and significant changes inmRNAexpression of apelin andAPJreceptor.
FAMILY MATTERS: EFFECTS OF FAMILY MEMBERS’ RESIDENTIAL AREAS ON CRIME LOCATION CHOICE*
Authors: MENTING BARBARA , LAMMERS MARRE , RUITER STIJN , BERNASCO WIM
Published: July 2016

According to crime pattern theory, offenders are likely to select crime locations within their awareness space. Previous studies have shown that offenders often commit crimes within their current and former residential areas and in areas they previously targeted. However, offenders’ awareness spaces obviously consist of more locations that potentially influence their crime location choices. This study examines the importance of the residential areas of offenders’ family members. Most offenders visit their families at least occasionally and consequently get familiar with the areas in which their families live. It is hypothesized that family members’ residential areas are at increased risk of being targeted. Unique data were used to reconstruct residential histories of the parents, siblings, and children of 7,910 offenders who committed 19,420 offenses. The results of discrete spatial choice models showed that residential areas of family members are indeed at increased risk of being targeted. Current familial residential areas had stronger and more consistent effects than had former familial residential areas. Effects were strongest for the residential areas of offenders’ children compared with those of their parents and siblings. The residential areas of male and female family members affected the crime location choices of male and female offenders equally.
A Comparison of Policy Instruments to Reduce Greenhouse Gas Emissions
Authors: Freebairn John
Published: July 2016

Tax, emission trading schemes, regulations and subsidy policy instruments to reduce Australian greenhouse gas emissions are assessed. Australian recent and proposed examples are used as illustrations. Comparative pollution reduction cost, tax interaction distortion costs, redistribution effects and operating cost properties are evaluated. A tax instrument with a comprehensive base, combined with recycling the revenue windfall to households, is argued to be a suitable guideline for future policy; some regulations to counter information and other market failures can be important complements.