bluuebunny/crossref_metadata_2025 huggingface dataset:
Fishing directly selects on growth rate via behaviour: implications of growth-selection that is independent of size
Authors: Biro Peter A. , Sampson Portia
Published: January 2015

Size-selective harvest of fish and crustacean populations has reduced stock numbers, and led to reduced growth rates and earlier maturation. In contrast to the focus on size-selective effects of harvest, here, we test the hypothesis that fishing may select on life-history traits (here, growth rate) via behaviour, even in the absence of size selection. If true, then traditional size-limits used to protect segments of a population cannot fully protect fast growers, because at any given size, fast-growers will be more vulnerable owing to bolder behaviour. We repeatedly measured individual behaviour and growth of 86 crayfish and found that fast-growing individuals were consistently bold and voracious over time, and were subsequently more likely to be harvested in single- and group-trapping trials. In addition, there was some indication that sex had independent effects on behaviour and trappability, whereby females tended to be less active, shyer, slower-growing and less likely to be harvested, but not all these effects were significant. This study represents, to our knowledge, the first across-individual support for this hypothesis, and suggests that behaviour is an important mechanism for fishing selectivity that could potentially lead to evolution of reduced intrinsic growth rates.
Genetic and phenotypic changes in an Atlantic salmon population supplemented with non-local individuals: a longitudinal study over 21 years
Authors: Le Cam Sabrina , Perrier Charles , Besnard Anne-Laure , Bernatchez Louis , Evanno Guillaume
Published: January 2015

While introductions and supplementations using non-native and potentially domesticated individuals may have dramatic evolutionary effects on wild populations, few studies documented the evolution of genetic diversity and life-history traits in supplemented populations. Here, we investigated year-to-year changes from 1989 to 2009 in genetic admixture at 15 microsatellite loci and in phenotypic traits in an Atlantic salmon (Salmo salar) population stocked during the first decade of this period with two genetically and phenotypically distinct source populations. We detected a pattern of temporally increasing introgressive hybridization between the stocked population and both source populations. The proportion of fish returning to the river after a single winter at sea (versusseveral ones) was higher in fish assigned to the main source population than in local individuals. Moreover, during the first decade of the study, both single-sea-winter and multi-sea-winter (MSW) fish assigned to the main source population were smaller than local fish. During the second decade of the study, MSW fish defined as hybrids were lighter and smaller than fish from parental populations, suggesting outbreeding depression. Overall, this study suggests that supplementation with non-local individuals may alter not only the genetic diversity of wild populations but also life-history traits of adaptive significance.
Romboutsia sedimentorum sp. nov., isolated from an alkaline-saline lake sediment and emended description of the genus Romboutsia
Authors: Wang Yanwei , Song Jinlong , Zhai Yi , Zhang Chi , Gerritsen Jacoline , Wang Huimin , Chen Xiaorong , Li Yanting , Zhao Bingqiang , Zhao Bin , Ruan Zhiyong
Published: January 2015

A Gram-stain-positive, spore-forming, obligately anaerobic bacterium, designated LAM201T, was isolated from sediment samples from an alkaline-saline lake located in Daqing oilfield, Daqing City, PR China. Cells of strain LAM201T were non-motile and straight or spiral rod-shapes. Strain LAM201T was able to utilize glucose, fructose, maltose, trehalose and sorbitol as the sole carbon source. Acetic acid, ethanol, iso-butanoic acid and iso-valeric acid were the main products of glucose fermentation. The major fatty acids of LAM201T were C16 : 0 (26.7 %) and C18 : 0 (11.2 %). The main polar lipids were four unknown glycolipids and five unknown phospholipids. The predominant cell-wall sugars were ribose and galactose. The cell-wall peptidoglycan of strain LAM201T contained alanine, glycine, glutamic acid and aspartic acid. Sodium sulfite was used as the electron acceptor. The G+C content of the genomic DNA was 32±0.8 mol%, as determined by the T
m method. Analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the genus

Romboutsia

and was most closely related to

Romboutsia lituseburensis

DSM 797T and

Romboutsia ilealis

CRIBT with 97.3 % and 97.2 % similarities, respectively. The DNA–DNA hybridization values between strain LAM201T and the two reference strains were 37 % and 31 %, respectively. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM201T is suggested to represent a novel species within the genus

Romboutsia

, for which the name Romboutsia sedimentorum sp. nov. is proposed. The type strain is LAM201T ( = ACCC 00717T = JCM 19607T).
The Arabidopsis Transcription Factor BRASSINOSTEROID INSENSITIVE1-ETHYL METHANESULFONATE-SUPPRESSOR1 Is a Direct Substrate of MITOGEN-ACTIVATED PROTEIN KINASE6 and Regulates Immunity
Authors: Kang Sining , Yang Fan , Li Lin , Chen Huamin , Chen She , Zhang Jie
Published: January 2015

Pathogen-associated molecular patterns (PAMPs) are recognized by plant pattern recognition receptors to activate PAMP-triggered immunity (PTI). Mitogen-activated protein kinases (MAPKs), as well as other cytoplasmic kinases, integrate upstream immune signals and, in turn, dissect PTI signaling via different substrates to regulate defense responses. However, only a few direct substrates of these signaling kinases have been identified. Here, we show that PAMP perception enhances phosphorylation of BRASSINOSTEROID INSENSITIVE1-ETHYL METHANESULFONATE-SUPPRESSOR1 (BES1), a transcription factor involved in brassinosteroid (BR) signaling pathway, through pathogen-induced MAPKs in Arabidopsis (Arabidopsis thaliana). BES1 interacts with MITOGEN-ACTIVATED PROTEIN KINASE6 (MPK6) and is phosphorylated by MPK6. bes1 loss-of-function mutants display compromised resistance to bacterial pathogen Pseudomonas syringae pv tomato DC3000. BES1 S286A/S137A double mutation (BES1SSAA) impairs PAMP-induced phosphorylation and fails to restore bacterial resistance in bes1 mutant, indicating a positive role of BES1 phosphorylation in plant immunity. BES1 is phosphorylated by glycogen synthase kinase3 (GSK3)-like kinase BR-insensitive2 (BIN2), a negative regulator of BR signaling. BR perception inhibits BIN2 activity, allowing dephosphorylation of BES1 to regulate plant development. However, BES1SSAA does not affect BR-mediated plant growth, suggesting differential residue requirements for the modulation of BES1 phosphorylation in PTI and BR signaling. Our study identifies BES1 as a unique direct substrate of MPK6 in PTI signaling. This finding reveals MAPK-mediated BES1 phosphorylation as another BES1 modulation mechanism in plant cell signaling, in addition to GSK3-like kinase-mediated BES1 phosphorylation and F box protein-mediated BES1 degradation.
Structural and biochemical analyses of theStreptococcus pneumoniaeL,D-carboxypeptidase DacB
Authors: Zhang Juan , Yang Yi-Hu , Jiang Yong-Liang , Zhou Cong-Zhao , Chen Yuxing
Published: January 2015

The L,D-carboxypeptidase DacB plays a key role in the remodelling ofStreptococcus pneumoniaepeptidoglycan during cell division. In order to decipher its substrate-binding properties and catalytic mechanism, the 1.71 Å resolution crystal structure of DacB fromS. pneumoniaeTIGR4 is reported. Structural analyses in combination with comparisons with the recently reported structures of DacB fromS. pneumoniaeD39 and R6 clearly demonstrate that DacB adopts a zinc-dependent carboxypeptidase fold and belongs to the metallopeptidase M15B subfamily. In addition, enzymatic activity assays further confirm that DacB indeed acts as an L,D-carboxypeptidase towards the tetrapeptide L-Ala-D-iGln-L-Lys-D-Ala of the peptidoglycan stem, withKmandkcatvalues of 2.84 ± 0.37 mMand 91.49 ± 0.05 s−1, respectively. Subsequent molecular docking and site-directed mutagenesis enable the assignment of the key residues that bind to the tetrapeptide. Altogether, these findings provide structural insights into substrate recognition in the metallopeptidase M15B subfamily.
The structure of the proteinaceous inhibitor PliI fromAeromonas hydrophilain complex with its target lysozyme
Authors: Leysen Seppe , Van Herreweghe Joris M. , Yoneda Kazunari , Ogata Makoto , Usui Taichi , Araki Tomohiro , Michiels Christiaan W. , Strelkov Sergei V.
Published: January 2015

Recent microbiological data have revealed that Gram-negative bacteria are able to protect themselves against the lytic action of host lysozymes by secreting proteinaceous inhibitors. Four distinct classes of such inhibitors have been discovered that specifically act against c-type, g-type and i-type lysozymes. Here, the 1.24 Å resolution crystal structure of the periplasmic i-type lysozyme inhibitor fromAeromonas hydrophila(PliI-Ah) in complex with the i-type lysozyme fromMeretrix lusoriais reported. The structure is the first to explain the inhibitory mechanism of the PliI family at the atomic level. A distinct `ridge' formed by three exposed PliI loops inserts into the substrate-binding groove of the lysozyme, resulting in a complementary `key–lock' interface. The interface is principally stabilized by the interactions made by the PliI-Ah residues Ser104 and Tyr107 belonging to the conserved SGxY motif, as well as by the other conserved residues Ser46 and Asp76. The functional importance of these residues is confirmed by inhibition assays with the corresponding point mutants of PliI-Ah. The accumulated structural data on lysozyme–inhibitor complexes from several classes indicate that in all cases an extensive interface of either a single or a double `key–lock' type is formed, resulting in highly efficient inhibition. These data provide a basis for the rational development of a new class of antibacterial drugs.
Data Exploration Toolkitfor serial diffraction experiments
Authors: Zeldin Oliver B. , Brewster Aaron S. , Hattne Johan , Uervirojnangkoorn Monarin , Lyubimov Artem Y. , Zhou Qiangjun , Zhao Minglei , Weis William I. , Sauter Nicholas K. , Brunger Axel T.
Published: January 2015

Ultrafast diffraction at X-ray free-electron lasers (XFELs) has the potential to yield new insights into important biological systems that produce radiation-sensitive crystals. An unavoidable feature of the `diffraction before destruction' nature of these experiments is that images are obtained from many distinct crystals and/or different regions of the same crystal. Combined with other sources of XFEL shot-to-shot variation, this introduces significant heterogeneity into the diffraction data, complicating processing and interpretation. To enable researchers to get the most from their collected data, a toolkit is presented that provides insights into the quality of, and the variation present in, serial crystallography data sets. These tools operate on the unmerged, partial intensity integration results from many individual crystals, and can be used on two levels: firstly to guide the experimental strategy during data collection, and secondly to help users make informed choices during data processing.
Density- and wavefunction-normalized Cartesian spherical harmonics forl≤ 20
Authors: Michael J. Robert , Volkov Anatoliy
Published: January 2015

The widely used pseudoatom formalism [Stewart (1976).Acta Cryst. A32, 565–574; Hansen & Coppens (1978).Acta Cryst.A34, 909–921] in experimental X-ray charge-density studies makes use of real spherical harmonics when describing the angular component of aspherical deformations of the atomic electron density in molecules and crystals. The analytical form of the density-normalized Cartesian spherical harmonic functions for up tol≤ 7 and the corresponding normalization coefficients were reported previously by Paturle & Coppens [Acta Cryst.(1988), A44, 6–7]. It was shown that the analytical form for normalization coefficients is available primarily forl≤ 4 [Hansen & Coppens, 1978; Paturle & Coppens, 1988; Coppens (1992).International Tables for Crystallography, Vol. B,Reciprocal space, 1st ed., edited by U. Shmueli, ch. 1.2. Dordrecht: Kluwer Academic Publishers; Coppens (1997).X-ray Charge Densities and Chemical Bonding. New York: Oxford University Press]. Only in very special cases it is possible to derive an analytical representation of the normalization coefficients for 4  4 the density normalization coefficients were calculated numerically to within seven significant figures. In this study we review the literature on the density-normalized spherical harmonics, clarify the existing notations, use the Paturle–Coppens (Paturle & Coppens, 1988) method in the WolframMathematicasoftware to derive the Cartesian spherical harmonics forl≤ 20 and determine the density normalization coefficients to 35 significant figures, and computer-generate a Fortran90 code. The article primarily targets researchers who work in the field of experimental X-ray electron density, but may be of some use to all who are interested in Cartesian spherical harmonics.
Group-theoretical analysis of aperiodic tilings from projections of higher-dimensional latticesBn
Authors: Koca Mehmet , Ozdes Koca Nazife , Koc Ramazan
Published: January 2015

A group-theoretical discussion on the hypercubic lattice described by the affine Coxeter–Weyl groupWa(Bn) is presented. When the lattice is projected onto the Coxeter plane it is noted that the maximal dihedral subgroupDhofW(Bn) withh= 2nrepresenting the Coxeter number describes theh-fold symmetric aperiodic tilings. Higher-dimensional cubic lattices are explicitly constructed forn= 4, 5, 6. Their rank-3 Coxeter subgroups and maximal dihedral subgroups are identified. It is explicitly shown that when their Voronoi cells are decomposed under the respective rank-3 subgroupsW(A3),W(H2) ×W(A1) andW(H3) one obtains the rhombic dodecahedron, rhombic icosahedron and rhombic triacontahedron, respectively. Projection of the latticeB4onto the Coxeter plane represents a model for quasicrystal structure with eightfold symmetry. TheB5lattice is used to describe both fivefold and tenfold symmetries. The latticeB6can describe aperiodic tilings with 12-fold symmetry as well as a three-dimensional icosahedral symmetry depending on the choice of subspace of projections. The novel structures from the projected sets of lattice points are compatible with the available experimental data.
The correlation between corporate governance and market value: regime or signal?
Authors: Li Chang , Zheng Wei , Chang Philip , Li Shanmin
Published: January 2015

Purpose

– As literatures argue that managers’ personalities will affect both corporate governance structures and corporate performance, the correlation between them is a mixed result. The purpose of this paper is to separate different routes leading to the mixed correlation, and name the separated routes as regime effect and signal effect.

Design/methodology/approach

– By theoretical analysis, the authors list three routes leading to the correlation between corporate governance and corporate performance. Routes 1 and 2 show that governance can directly and indirectly change the performance; while route 3 shows that both the governance and performance are results of managers’ personalities, and the governance has no influence onto the performance, which means the correlation led by route 3 is fake. By design a new econometric methodology, this paper separates the mixed correlation between corporate governance and performance, and names the correlation led by routes 1 and 2 as the regime effect and the correlation led by route 3 as signal effect.

Findings

– By an empirical research on Chinese listed corporates, the authors find that the correlations between Chinese listed corporates’ market value and main corporate governance factors can be separated into regime effects and signal effects; and the authors also find that some factors (Share of Institutional Investors, Share of Real Controller and the Squared, Dummy of Identical CEO and Chairman, Ownership Concentration) only show regime effects, some factors (Separating Extent of Ownership and Controlling Right, Dummy of Provincial State-Owned Firms) only show signal effects, and some factors (Dummy of Republic State-Owned Firms, Scale of Board) show both. What’s more, the authors find out an interesting result that the state-owning has no negative regime effect on China SOEs’ performance but very significantly negative signal effect; in this paper, the authors suggest that this means the key negative factors of Chinese SOEs is not state-owning ownership structure but the managers’ corruption.

Practical implications

– As only the factors with regime effects can directly and indirectly affect corporates’ performance and the factors with signal effects show that there’re some managers’ personalities affecting both the governance and performance, the separation method in this paper can help shareholders knowing which governance factors will be helpful to improve the performance and which others will show managers’ hard-working or corruption intention.

Originality/value

– Separate the regime effect and the signal effect from the correlation between corporate governance and performance.
The role of psychopathy factors in reactive aggression within a sample of prisoners
Authors: Debowska Agata , Zeyrek Rios Emek Yuce
Published: January 2015

Purpose

– The purpose of this paper is to examine the role of four psychopathy factors (Interpersonal Manipulation (IPM), Callous Affect (CA), Erratic Lifestyle (ELS), and Antisocial Behaviour (ASB)) and the length of incarceration in reactive aggression. The predictive effect of dissatisfaction with peer relations, childhood experiences of violence, and criminal friends on reactive forms of aggressive acts is also explored.

Design/methodology/approach

– In total, 129 (n=129) male prisoners incarcerated in Stargard Szczecinski Prison were recruited for the study. Cross-sectional design using self-report questionnaire of retrospective and prospective nature was utilised.

Findings

– Hierarchical multiple regression analysis revealed that only one psychopathy facet, IPM, forms a significant association with reactive aggression. Another accurate correlate of reactive aggression was the length of incarceration.

Originality/value

– The results of the present study indicate that the commonly suggested two-factor models of psychopathy may be misguided. Future studies examining the effect of psychopathy facets on aggression should consider IPM and CA as separate dimensions. Additionally, this study is the first to demonstrate that reactive aggression may be exacerbated during incarceration.
Innovation in clusters: exploration capacity, networking intensity and external resources
Authors: Expósito-Langa Manuel , Tomás-Miquel José-Vicente , Molina-Morales F. Xavier
Published: January 2015

Purpose

– The purpose of this paper is to present an integrated model of the determinants of innovation in clusters. In the understanding, internal, external and relational dimensions must be considered to make up a complete picture of the innovation processes. The authors propose that the exploration capacity of the firm, as well as its networking intensity and the external resources provided by supporting organizations are relevant in this context.

Design/methodology/approach

– The empirical study has drawn on the population of the firms belonging to the Valencian textile industrial cluster in Spain and was carried out in two different phases. In the first step the authors applied the social network analysis technique to study the relational structure of the participating companies, followed by a second analysis aimed at performing a more detailed analysis of the companies that answered the roster by means of face-to-face interviews.

Findings

– Results suggest that firms in clusters must develop individual capacities parallel to the systemic resources in order to improve their innovation performance. These systemic resources are provided by the position in the knowledge network and the relations with Knowledge Intensive Business Services (KIBS), as agents that connect the cluster with external networks.

Originality/value

– In spite of diverse contributions, previous research only provides a partial explanation of the issue and others underestimate one of the elements (internal or external to the firm) where the sources of innovation are generated. The originality of this study lies in the fact that it presents a complete perspective of the innovation process in clustered firms and clarifies key questions in cluster studies through network analysis techniques.
Scalable decision support for digital preservation: an assessment
Authors: Becker Christoph , Faria Luis , Duretec Kresimir
Published: January 2015

Purpose

– This article aims to evaluate a new architecture for scalable decision-making and control in preservation environments for its ability to address five key goals: scalable content profiling; monitoring of compliance, risks and opportunities; efficient creation of trustworthy plans; context awareness; and loosely coupled preservation ecosystems. Scalable decision support and business intelligence capabilities are required to effectively secure content over time.

Design/methodology/approach

– We conduct a systematic evaluation of the contributions of the SCAPE Planning and Watch suite to provide effective and scalable decision support capabilities. We discuss the quantitative and qualitative evaluation of advancing the state of art and report on a case study with a national library.

Findings

– The system provides substantial capabilities for semi-automated, scalable decision-making and control of preservation functions in repositories. Well-defined interfaces allow a flexible integration with diverse institutional environments. The free and open nature of the tool suite further encourages global take-up in the repository communities.

Research limitations/implications

– The article discusses a number of bottlenecks and factors limiting the real-world scalability of preservation environments. This includes data-intensive processing of large volumes of information, automated quality assurance for preservation actions, and the element of human decision-making. We outline open issues and future work.

Practical implications

– The open nature of the software suite enables stewardship organizations to integrate the components with their own preservation environments and to contribute to the ongoing improvement of the systems.

Originality/value

– The paper reports on innovative research and development to provide preservation capabilities. The results of the assessment demonstrate how the system advances the control of digital preservation operations fromad hocdecision-making to proactive, continuous preservation management, through a context-aware planning and monitoring cycle integrated with operational systems.
Establishing of a Slovenian open access infrastructure: a technical point of view
Authors: Ojsteršek Milan , Brezovnik Janez , Kotar Mojca , Ferme Marko , Hrovat Goran , Bregant Albin , Borovič Mladen
Published: January 2015

Purpose

– The purpose of this paper is to present a technical perspective when implementing the Slovenian open access infrastructure that consists of four institutional repositories (IRs) and a national portal (NP) that aggregates content from the repositories in order to provide a common search engine, recommendations of similar documents, and similar text detection.

Design/methodology/approach

– During the project, the necessary legal background and processes for mandatory submissions of final study works, research publications and research data were established, as well as processes for data exchange between the IRs and the NP, and processes for similar text detection.

Findings

– The consortium consisted of four Slovenian universities that significantly differ in size, organisation, and workflows. It was anticipated that exactly the same legal background and software would be used for the four repositories. It turned out that complete unification was impossible due to the differences.

Practical implications

– The national open access infrastructure will improve the visibility of Slovenian research organisations. It supports the compliance with the funders’ open access mandates. The established infrastructure enables the depositing and archiving of approximately 80 percent of the peer-reviewed scientific publications that are annually published by Slovenian researchers. At the same time, the majority of final study works from Slovenian higher education institutions are available in full-text format.

Originality/value

– This paper describes a technical perspective for setting up a national open access infrastructure, which has not been described in the literature previously.
The D-NET software toolkit
Authors: Manghi Paolo , Artini Michele , Atzori Claudio , Bardi Alessia , Mannocci Andrea , La Bruzzo Sandro , Candela Leonardo , Castelli Donatella , Pagano Pasquale
Published: January 2015

Purpose

– The purpose of this paper is to present the architectural principles and the services of the D-NET software toolkit. D-NET is a framework where designers and developers find the tools for constructing and operating aggregative infrastructures (systems for aggregating data sources with heterogeneous data models and technologies) in a cost-effective way. Designers and developers can select from a variety of D-NET data management services, can configure them to handle data according to given data models, and can construct autonomic workflows to obtain personalized aggregative infrastructures.

Design/methodology/approach

– The paper provides a definition of aggregative infrastructures, sketching architecture, and components, as inspired by real-case examples. It then describes the limits of current solutions, which find their lacks in the realization and maintenance costs of such complex software. Finally, it proposes D-NET as an optimal solution for designers and developers willing to realize aggregative infrastructures. The D-NET architecture and services are presented, drawing a parallel with the ones of aggregative infrastructures. Finally, real-cases of D-NET are presented, to show-case the statement above.

Findings

– The D-NET software toolkit is a general-purpose service-oriented framework where designers can construct customized, robust, scalable, autonomic aggregative infrastructures in a cost-effective way. D-NET is today adopted by several EC projects, national consortia and communities to create customized infrastructures under diverse application domains, and other organizations are enquiring for or are experimenting its adoption. Its customizability and extendibility make D-NET a suitable candidate for creating aggregative infrastructures mediating between different scientific domains and therefore supporting multi-disciplinary research.

Originality/value

– D-NET is the first general-purpose framework of this kind. Other solutions are available in the literature but focus on specific use-cases and therefore suffer from the limited re-use in different contexts. Due to its maturity, D-NET can also be used by third-party organizations, not necessarily involved in the software design and maintenance.
An investigation into the perceptions of academic librarians and students towards next-generation OPACs and their features
Authors: Osborne Hollie M. , Cox Andrew
Published: January 2015

Purpose

– The purpose of this paper is to determine whether features of next-generation Online Public Access Catalogue (OPAC) interfaces are useful and intuitive to users who have different levels of searching ability. In addition, it investigates whether there is a difference between librarians’ and students’ preferences for specific features.

Design/methodology/approach

– The research is based on 18 semi-structured interviews conducted in July 2012 with three groups of library users from The University of Sheffield: librarians; Master of Arts Librarianship students; and a group of other post-graduate students.

Findings

– Overall, this study suggests that while the next-generation catalogue interfaces and features are useful, they are not as “intuitive” as some previous studies have claimed. Interviewees appeared to prefer the searching and browsing options over the Web 2.0 features. Both librarians and students have similar opinions regarding the usefulness of next-generation OPAC features, but preferences are complex.

Research limitations/implications

– The study is based on one institution, and the disciplinary background of the post-graduate students was limited.

Practical implications

– Promoting next generation OPACs and explaining their features to users is essential.

Originality/value

– The paper adds to the understanding of users’ preferences in relation to next-generation OPACs, locating the findings of the current findings firmly in the context of previous literature.
Enhancing the management of unstructured data in e-learning systems using MongoDB
Authors: Stevic Milorad Pantelija , Milosavljevic Branko , Perisic Branko Rade
Published: January 2015

Purpose

– Current e-learning platforms are based on relational database management systems (RDBMS) and are well suited for handling structured data. However, it is expected from e-learning solutions to efficiently handle unstructured data as well. The purpose of this paper is to show an alternative to current solutions for unstructured data management.

Design/methodology/approach

– Current repository-based solution for file management was compared to MongoDB architecture according to their functionalities and characteristics. This included several categories: data integrity, hardware acquisition, processing files, availability, handling concurrent users, partition tolerance, disaster recovery, backup policies and scalability.

Findings

– This paper shows that it is possible to improve e-learning platform capabilities by implementing a hybrid database architecture that incorporates RDBMS for handling structured data and MongoDB database system for handling unstructured data.

Research limitations/implications

– The study shows an acceptable adoption of MongoDB inside a service-oriented architecture (SOA) for enhancing e-learning solutions.

Practical implications

– This research enables an efficient file handling not only for e-learning systems, but also for any system where file handling is needed.

Originality/value

– It is expected that future single/joint e-learning initiatives will need to manage huge amount of files and they will require effective file handling solution. The new architecture solution for file handling is offered in this paper: it is different from current solutions because it is less expensive, more efficient, more flexible and requires less administrative and development effort for building and maintaining.
Impact of cancer on the effectiveness of cardiac Troponin I to predict right ventricular dysfunction in acute pulmonary embolism
Authors: Keller Karsten , Geyer Martin , Beule Johannes , Coldewey Meike , Balzer Jörn Oliver , Dippold Wolfgang
Published: January 2015

Background

Deep vein thrombosis (DVT) and pulmonary embolism (PE) are connected with a poor outcome in cancer patients. We aimed to investigate the impact of cancer on the effectiveness of cardiac Troponin I (cTnI) to predict right ventricular dysfunction (RVD) in acute PE.

Methods

We retrospectively analyzed the data of 182 patients with confirmed PE. PE patients were subdivided into two groups: (i) with concomitant active cancer disease or history of cancer, and (ii) without known cancer. Receiver operating characteristic (ROC) curves with area under the curve (AUC) was calculated for cTnI predicting RVD and related cut‐off levels for both groups.

Results

Thirty‐seven PE patients (20.3%) had an active cancer disease or a history of cancer. In contrast, 145 (79.7%) of the included PE patients did not have a known cancer disease or a history of cancer.

In the PE group with cancer, analysis of the ROC curve showed an AUC of 0.76 for cTnI predicting RVD with an optimal cut‐off value of 0.04 ng/mL; the risk of misclassification was 25.0%. In the PE group without cancer, AUC was 0.81 for cTnI predicting RVD with an optimal cut‐off value of 0.015 ng/mL; the risk of misclassification was 24.9%.

Conclusions

cTnI is effective for predicting RVD in PE patients with and without cancer. However, the effectiveness of cTnI to predict RVD was higher in PE patients without cancer than in those with cancer or a history of cancer.
Distribution and genetic diversity of Tomato spotted wilt virus following an incursion into Kenya
Authors: Macharia I. , Backhouse D. , Ateka E.M. , Wu S.‐B. , Harvey J. , Njahira M. , Skilton R.A.
Published: January 2015

Tomato spotted wilt virus (TSWV) affects the production of many horticultural crops worldwide. It was first reported from Kenya in 1999. The occurrence, distribution and genetic diversity of TSWV were evaluated in four tomato production areas in Kenya a decade after this incursion. The awareness of TSWV and its vectors among farmers was assessed through a questionnaire while plant samples including tomato leaves and fruit were collected from diseased and non‐diseased plants. The samples were assayed for TSWV using ELISA and reverse transcriptase‐polymerase chain reaction, and the resulting positive samples were sequenced. There was less awareness of the virus, its vectors and alternate hosts among farmers, despite the occurrence of the disease for over a decade. A total of 89 of 408 tomato samples tested positive for TSWV. Most of the positive samples came from Nakuru, where the virus was first detected, with only a single positive sample being obtained from Loitokitok and none from Bungoma or Kirinyaga. A phylogenetic analysis based on partial nucleocapsid (N) protein gene sequences suggested that the Kenyan isolates formed a single subgroup nested within a cluster of isolates that came predominantly from Europe. This indicated a single introduction that had undergone limited diversification. The study revealed that the disease has persisted in the area to which it was first introduced but has had very limited dispersal to other areas.
Intra‐individual reaction time variability based on ex‐Gaussian distribution as a potential endophenotype for attention‐deficit/hyperactivity disorder
Authors: Lin H.‐Y. , Hwang‐Gu S.‐L. , Gau S. S.‐F.
Published: January 2015

Objective

Intra‐individual variability in reaction time (IIV‐RT), defined by standard deviation of RT (RTSD), is considered as an endophenotype for attention‐deficit/hyperactivity disorder (ADHD). Ex‐Gaussian distributions of RT, rather than RTSD, could better characterize moment‐to‐moment fluctuations in neuropsychological performance. However, data of response variability based on ex‐Gaussian parameters as an endophenotypic candidate for ADHD are lacking.

Method

We assessed 411 adolescents with clinically diagnosed ADHD based on the DSM‐IV‐TR criteria as probands, 138 unaffected siblings, and 138 healthy controls. The output parameters, mu, sigma, and tau, of an ex‐Gaussian RT distribution were derived from the Conners' continuous performance test. Multi‐level models controlling for sex, age, comorbidity, and use of methylphenidate were applied.

Results

Compared with unaffected siblings and controls, ADHD probands had elevated sigma value, omissions, commissions, and mean RT. Unaffected siblings formed an intermediate group in‐between probands and controls in terms of tau value and RTSD. There was no between‐group difference in mu value. Conforming to a context‐dependent nature, unaffected siblings still had an intermediate tau value in‐between probands and controls across different interstimulus intervals.

Conclusion

Our findings suggest IIV‐RT represented by tau may be a potential endophenotype for inquiry into genetic underpinnings of ADHD in the context of heterogeneity.
Pharmacogenetics of plasma efavirenz exposure in HIV‐infected adults and children in South Africa
Authors: Sinxadi Phumla Z. , Leger Paul D. , McIlleron Helen M. , Smith Peter J. , Dave Joel A. , Levitt Naomi S , Maartens Gary , Haas David W.
Published: January 2015

Aims

Genetic factors, notably CYP2B6 516G→T [rs3745274] and 983T→C [rs28399499], explain much of the interindividual variability in efavirenz pharmacokinetics, but data from Africa are limited. We characterized relationships between genetic polymorphisms and plasma efavirenz concentrations in HIV‐infected Black South African adults and children.

Methods

Steady‐state mid‐dosing interval efavirenz concentrations were measured. We genotyped 241 polymorphisms in genes potentially relevant to efavirenz metabolism and transport, including ABCB1, CYP2A6, CYP2B6, CYP3A4, CYP3A5, NR1I2 and NR1I3.

Results

Among 113 participants (59 adults and 54 children), minor allele frequencies for CYP2B6 516G→T, 983T→C, and 15582C→T [rs4803419] were 0.36, 0.07, and 0.09, respectively. Based on composite CYP2B6 15582/516/983 genotype, there were 33 extensive metabolizer, 62 intermediate metabolizer and 18 slow metabolizer genotypes. Median (IQR) mid‐dose efavirenz concentrations were 1.44 (1.21–1.93) µg ml–1, 2.08 (1.68–2.94) µg ml–1 and 7.26 (4.82–8.34) µg ml–1 for extensive, intermediate and slow metabolizers, respectively. In univariate analyses, a model that included composite genotype best predicted efavirenz concentrations (β = 0.28, 95% CI 0.21, 0.35, P = 2.4 × 10–11). Among individual CYP2B6 polymorphisms, 516G→T best predicted efavirenz concentrations (β = 0.22, 95% CI 0.13, 0.30, P = 1.27 × 10−6). There was also associations with 983T→C (β = 0.27, 95% CI 0.10, 0.44, P = 0.002) and 15582C→T (β = 0.11, 95% CI 0.01, 0.22, P = 0.04). Associations were consistent in adults and children. No other polymorphisms were independently associated with efavirenz concentrations.

Conclusions

Composite CYP2B6 genotype based on CYP2B6 516G→T, 983T→C, and 15582C→T best described efavirenz exposure in HIV‐infected Black South African adults and children.
Fault‐controlled fluid flow inferred from hydrothermal vents imaged in 3D seismic reflection data, offshore NW Australia
Authors: Magee Craig , Duffy Oliver B. , Purnell Kirsty , Bell Rebecca E. , Jackson Christopher A.‐L. , Reeve Matthew T.
Published: January 2015

Fluid migration pathways in the subsurface are heavily influenced by pre‐existing faults. Although studies of active fluid‐escape structures can provide insights into the relationships between faults and fluid flow, they cannot fully constrain the geometry of and controls on the contemporaneous subsurface fluid flow pathways. We use 3D seismic reflection data from offshore NW Australia to map 121 ancient hydrothermal vents, likely related to magmatic activity, and a normal fault array considered to form fluid pathways. The buried vents consist of craters up to 264 m deep, which host a mound of disaggregated sedimentary material up to 518 m thick. There is a correlation between vent alignment and underlying fault traces. Seismic‐stratigraphic observations and fault kinematic analyses reveal that the vents were emplaced on an intra‐Tithonian seabed in response to the explosive release of fluids hosted within the fault array. We speculate that during the Late Jurassic the convex‐upwards morphology of the upper tip‐lines of individual faults acted to channelize ascending fluids and control where fluid expulsion and vent formation occurred. This contribution highlights the usefulness of 3D seismic reflection data to constraining normal fault‐controlled subsurface fluid flow.
Ginkgetin inhibits the growth of DU−145 prostate cancer cells through inhibition of signal transducer and activator of transcription 3 activity
Authors: Jeon Yoon Jung , Jung Seung‐Nam , Yun Jieun , Lee Chang Woo , Choi Jiyeon , Lee Yu‐Jin , Han Dong Cho , Kwon Byoung‐Mog
Published: January 2015

Signal transducer and activator of transcription 3 (STAT3) is constitutively activated in human cancers. Therefore, STAT3 is a therapeutic target of cancer drug discovery. We previously reported that natural products inhibited constitutively activated STAT3 in human prostate tumor cells. We used a dual‐luciferase assay to screen 200 natural products isolated from herbal medicines and we identified ginkgetin obtained from the leaves of Ginkgo biloba L. as a STAT3 inhibitor. Ginkgetin inhibited both inducible and constitutively activated STAT3 and blocked the nuclear translocation of p‐STAT3 in DU‐145 prostate cancer cells. Furthermore, ginkgetin selectively inhibited the growth of prostate tumor cells stimulated with activated STAT3. Ginkgetin induced STAT3 dephosphorylation at Try705 and inhibited its localization to the nucleus, leading to the inhibition of expression of STAT3 target genes such as cell survival‐related genes (cyclin D1 and survivin) and anti‐apoptotic proteins (Bcl‐2 and Bcl‐xL). Therefore, ginkgetin inhibited the growth of STAT3‐activated tumor cells. We also found that ginkgetin inhibited tumor growth in xenografted nude mice and downregulated p‐STAT3Tyr705 and survivin in tumor tissues. This is the first report that ginkgetin exerts antitumor activity by inhibiting STAT3. Therefore, ginkgetin is a good STAT3 inhibitor and may be a useful lead molecule for development of a therapeutic STAT3 inhibitor.
Surgical Stress Induces Brain‐Derived Neurotrophic Factor Reduction and Postoperative Cognitive Dysfunction Via Glucocorticoid Receptor Phosphorylation in Aged Mice
Authors: Tian Xiao‐Sheng , Tong Ya‐Wei , Li Zheng‐Qian , Li Lun‐Xu , Zhang Tao , Ren Tian‐Yun , Zhou Ting , Wang He‐Cheng , Zhan Rui , Sun Yang , Yan Zhao , Wang Qiu‐Dian , Fan Dong‐Sheng , Kong Fan‐Jun , Guo Xiang‐Yang , Xiao Wei‐Zhong , Chui De‐Hua
Published: January 2015

Aims

This study explored whether surgical stress‐induced glucocorticoid receptor (GR) phosphorylation is related to postoperative cognitive dysfunction (POCD) in aged individuals. Inhibition of GR activation could be an effective treatment for POCD.

Methods

A laparotomy was given to C57/BL6 mice in POCD group both 20 and 6 months old. Animals in control group were treated in identical manners except for laparotomy. Cognitive function was evaluated by Morris water maze and elevated plus maze. Western blot and Elisa assay were used to detect related molecules. Mifepristone and roscovitine were treated as inhibitions of GR phosphorylation.

Results

The cognitive function was impaired, and brain‐derived neurotrophic factor (BDNF) was found reduced in aged POCD group. GR translocation into nucleus and elevated GR phosphorylation were found in prefrontal cortex of aged POCD mice. Cyclin‐dependent Kinase 5 (CDK5), kinase for GR phosphorylation also elevated in aged POCD mice. With GR antagonist and CDK5 inhibitor, reduction of BDNF and cognitive dysfunction in aged mice were both rescued.

Conclusion

These results presented a mechanism that surgical stress‐induced GR phosphorylation contributes to POCD in aged individuals. Inhibition of GR activation and phosphorylation might be a potential treatment target of POCD.
Clinical evaluation of new diagnostic modalities of endoscopic ultrasound for pancreaticobiliary diseases
Authors: Teoh Anthony Yuen Bun , Tang Raymond Shing Yan
Published: January 2015

Endoscopic ultrasonography (EUS) is currently an integral tool for work‐up of pancreaticobiliary neoplasms. Tissue acquisition by EUS is possible with fine‐needle aspiration (FNA) cytology and histology. However, FNA still carries some limitations and risks of complications. The use of image‐enhanced EUS may improve detection and characterization of pancreaticobiliary neoplasms and complement FNA. The present article aims to provide an overview of the current development of contrast‐enhanced imaging and elastography in EUS and their potential application in the diagnosis of pancreaticobiliary diseases.
Improved visibility of colorectal flat tumors using image‐enhanced endoscopy
Authors: Oka Shiro , Tamai Naoto , Ikematsu Hiroaki , Kawamura Takuji , Sawaya Manabu , Takeuchi Yoji , Uraoka Toshio , Moriyama Tomohiko , Kawano Hiroshi , Matsuda Takahisa
Published: January 2015

Colonoscopy is considered the gold standard for detecting colorectal tumors; however, conventional colonoscopy can miss flat tumors. We aimed to determine whether visualization of colorectal flat lesions was improved by autofluorescence imaging and narrow‐band imaging image analysis in conjunction with a new endoscopy system. Eight physicians compared autofluorescent, narrow‐band, and chromoendoscopy images to 30 corresponding white‐light images of flat tumors. Physicians rated tumor visibility from each image set as follows: +2 (improved), +1 (somewhat improved), 0 (equivalent to white light), −1 (somewhat decreased), and −2 (decreased). The eight scores for each image were totalled and evaluated. Interobserver agreement was also examined. Autofluorescent, narrow‐band, and chromoendoscopy images showed improvements of 63.3% (19/30), 6.7% (2/30), and 73.3% (22/30), respectively, with no instances of decreased visibility. Autofluorescence scores were generally greater than narrow‐band scores. Interobserver agreement was 0.65 for autofluorescence, 0.80 for narrow‐band imaging, and 0.70 for chromoendoscopy. In conclusion, using a new endoscopy system in conjunction with autofluorescent imaging improved visibility of colorectal flat tumors, equivalent to the visibility achieved using chromoendoscopy.
Right and Left Atrial Dissimilarities in Normal Subjects Explored by Speckle Tracking Echocardiography
Authors: Moustafa Sherif , Zuhairy Hamed , Youssef Mostafa A. , Alvarez Nanette , Connelly Michael S. , Prieur Timothy , Mookadam Farouk
Published: January 2015

Background

Atrial function is an important contributor of ventricular function and has a prognostic role in various cardiovascular diseases. We tested the hypothesis that right and left atrial (RA & LA) function may not be equal despite their accommodating identical cardiac output.

Methods

Two‐dimensional (2D) speckle tracking echocardiography was acquired from the apical four‐chamber view in 100 normal subjects. Both RA/LA subendocardial borders were traced to obtain atrial volumes, strain (ε) and strain rate (SR). Reservoir, conduit, and booster pump functions were evaluated. Consequently, εNeg (corresponding to pump function) and εPos (corresponding to conduit function) were gauged. The SR parameters (SRLateNeg, SRPos, and SREarlyNeg), corresponding respectively to atrial systole, inception of ventricular systole, and inception of ventricular diastole, were measured.

Results

Mean age was 39 ± 15 years with 50 men (50%). Volumetric indices revealed that reservoir (Filling Volume = 35.1 ± 10.4 mL for LA vs. 27.47 ± 11.93 mL for RA, expansion index = 52.18 ± 16.89% for LA vs. 45.03 ± 16.49% for RA and diastolic emptying index = 52.85 ± 16.85 for LA vs. 45.62 ± 16.5 for RA, P < 0.001) and conduit (passive emptying (%) of total emptying = 34.49 ± 10.4 for LA vs. 26.82 ± 11.98 for RA and passive emptying index = 52.63 ± 16.86 for LA vs. 45.39 ± 16.5 for RA, P < 0.001) functions were significantly higher in the LA compared to the RA. Nevertheless, deformation indices demonstrated an opposite pattern (SRpos = 1.88 ± 0.74 for RA vs. 1.56 ± 0.54 for LA, P = 0.03 and εPos = 59.56 ± 30.63 for RA vs. 45.94 ± 16.67 for LA, P < 0.001). Reservoir, conduit, and booster pump functions showed no statistical significance among both genders.

Conclusions

Evaluation of global and regional RA/LA function by speckle tracking echocardiography is feasible. The current report provides insights regarding dissimilarities between both atria in healthy individuals. The significance of these findings and their potential application will warrant further work.