bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parkinson-related LRRK2 mutation R1441C/G/H impairs PKA phosphorylation of LRRK2 and disrupts its interaction with 14-3-3
Authors: Muda Kathrin , Bertinetti Daniela , Gesellchen Frank , Hermann Jennifer Sarah , von Zweydorf Felix , Geerlof Arie , Jacob Anette , Ueffing Marius , Gloeckner Christian Johannes , Herberg Friedrich W. 
Published: December 2013

Significance
Leucine-rich repeat kinase 2 (LRRK2) is a multidomain protein implicated in Parkinson disease, and cAMP-dependent protein kinase (PKA) has been suggested to act as an upstream kinase phosphorylating LRRK2. Using a phosphoproteomics approach, we identified several novel PKA phosphorylation sites on LRRK2. We could demonstrate that one PKA phosphosite comprises the second most common mutation in LRRK2 (R1441C/G/H) attributed to Parkinson disease. Our findings reveal that this site is mandatory for subsequent 14-3-3 binding and affects LRRK2 kinase activity. These data provide a mechanistic insight into the regulation of LRRK2 kinase activity and its perturbation by disease-associated mutations.
Wigwams: identifying gene modules co-regulated across multiple biological conditions
Authors: Polanski Krzysztof , Rhodes Johanna , Hill Claire , Zhang Peijun , Jenkins Dafyd J. , Kiddle Steven J. , Jironkin Aleksey , Beynon Jim , Buchanan-Wollaston Vicky , Ott Sascha , Denby Katherine J. 
Published: December 2013

AbstractMotivation: Identification of modules of co-regulated genes is a crucial first step towards dissecting the regulatory circuitry underlying biological processes. Co-regulated genes are likely to reveal themselves by showing tight co-expression, e.g. high correlation of expression profiles across multiple time series datasets. However, numbers of up- or downregulated genes are often large, making it difficult to discriminate between dependent co-expression resulting from co-regulation and independent co-expression. Furthermore, modules of co-regulated genes may only show tight co-expression across a subset of the time series, i.e. show condition-dependent regulation.Results: Wigwams is a simple and efficient method to identify gene modules showing evidence for co-regulation in multiple time series of gene expression data. Wigwams analyzes similarities of gene expression patterns within each time series (condition) and directly tests the dependence or independence of these across different conditions. The expression pattern of each gene in each subset of conditions is tested statistically as a potential signature of a condition-dependent regulatory mechanism regulating multiple genes. Wigwams does not require particular time points and can process datasets that are on different time scales. Differential expression relative to control conditions can be taken into account. The output is succinct and non-redundant, enabling gene network reconstruction to be focused on those gene modules and combinations of conditions that show evidence for shared regulatory mechanisms. Wigwams was run using six Arabidopsis time series expression datasets, producing a set of biologically significant modules spanning different combinations of conditions.Availability and implementation: A Matlab implementation of Wigwams, complete with graphical user interfaces and documentation, is available at: warwick.ac.uk/wigwams.Contact: k.j.denby@warwick.ac.ukSupplementary Data: Supplementary data are available at Bioinformatics online.
Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package
Authors: Rodrigue Nicolas , Lartillot Nicolas 
Published: December 2013

Abstract
Motivation: In recent years, there has been an increasing interest in the potential of codon substitution models for a variety of applications. However, the computational demands of these models have sometimes lead to the adoption of oversimplified assumptions, questionable statistical methods or a limited focus on small data sets.
Results: Here, we offer a scalable, message-passing-interface-based Bayesian implementation of site-heterogeneous codon models in the mutation-selection framework. Our software jointly infers the global mutational parameters at the nucleotide level, the branch lengths of the tree and a Dirichlet process governing across-site variation at the amino acid level. We focus on an example estimation of the distribution of selection coefficients from an alignment of several hundred sequences of the influenza PB2 gene, and highlight the site-specific characterization enabled by such a modeling approach. Finally, we discuss future potential applications of the software for conducting evolutionary inferences.
Availability and implementation: The models are implemented within the PhyloBayes-MPI package, (available at phylobayes.org) along with usage details in the accompanying manual.
Contact: nicolas.rodrigue@ucalgary.ca
Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome
Authors: Philippe Nicolas , Bou Samra Elias , Boureux Anthony , Mancheron Alban , Rufflé Florence , Bai Qiang , De Vos John , Rivals Eric , Commes Thérèse 
Published: December 2013

Abstract
Recent sequencing technologies that allow massive parallel production of short reads are the method of choice for transcriptome analysis. Particularly, digital gene expression (DGE) technologies produce a large dynamic range of expression data by generating short tag signatures for each cell transcript. These tags can be mapped back to a reference genome to identify new transcribed regions that can be further covered by RNA-sequencing (RNA-Seq) reads. Here, we applied an integrated bioinformatics approach that combines DGE tags, RNA-Seq, tiling array expression data and species-comparison to explore new transcriptional regions and their specific biological features, particularly tissue expression or conservation. We analysed tags from a large DGE data set (designated as ‘TranscriRef’). We then annotated 750 000 tags that were uniquely mapped to the human genome according to Ensembl. We retained transcripts originating from both DNA strands and categorized tags corresponding to protein-coding genes, antisense, intronic- or intergenic-transcribed regions and computed their overlap with annotated non-coding transcripts. Using this bioinformatics approach, we identified ∼34 000 novel transcribed regions located outside the boundaries of known protein-coding genes. As demonstrated using sequencing data from human pluripotent stem cells for biological validation, the method could be easily applied for the selection of tissue-specific candidate transcripts. DigitagCT is available at http://cractools.gforge.inria.fr/softwares/digitagct.
Nucleosomes accelerate transcription factor dissociation
Authors: Luo Yi , North Justin A. , Rose Sean D. , Poirier Michael G. 
Published: December 2013

AbstractTranscription factors (TF) bind DNA-target sites within promoters to activate gene expression. TFs target their DNA-recognition sequences with high specificity by binding with resident times of up to hours in vitro. However, in vivo TFs can exchange on the order of seconds. The factors that regulate TF dynamics in vivo and increase dissociation rates by orders of magnitude are not known. We investigated TF binding and dissociation dynamics at their recognition sequence within duplex DNA, single nucleosomes and short nucleosome arrays with single molecule total internal reflection fluorescence (smTIRF) microscopy. We find that the rate of TF dissociation from its site within either nucleosomes or nucleosome arrays is increased by 1000-fold relative to duplex DNA. Our results suggest that TF binding within chromatin could be responsible for the dramatic increase in TF exchange in vivo. Furthermore, these studies demonstrate that nucleosomes regulate DNA–protein interactions not only by preventing DNA–protein binding but by dramatically increasing the dissociation rate of protein complexes from their DNA-binding sites.
Direct Reciprocity Under Uncertainty Does Not Explain One-Shot Cooperation, But It Can Explain Norm Psychology
Authors: Zefferman Matthew R. 
Published: December 2013

AbstractHumans in many societies cooperate in economic experiments at much higher levels than would be expected if their goal was maximizing economic returns even when interactions are anonymous and one-shot. This is a puzzle because paying a cost to benefit another player in one-shot interactions has no direct benefit to the cooperator. This paper explores the logic of two competing evolutionary hypotheses to explain this behavior. The “norm psychology” hypothesis holds that a player’s choice of strategy is heavily influenced by socially-learned cultural norms. Its premise is that over the course of human evolutionary history, cultural norms varied considerably across human societies and through a process of gene-culture co-evolution, humans evolved mechanisms to learn and adopt the norms of their particular society. The “evolutionary mismatch” hypothesis holds that pro-social preferences evolved genetically in our hunter-gatherer past where one-shot anonymous interactions were rare and these evolved “protocols” for cooperation are misapplied in modern, laboratory, conditions. I compare these hypotheses by adopting a well-known model of the mismatch hypothesis. I show that the cooperation generated by the model is based on a flawed assumption - that the best thing to do is cooperate in a repeated game. I show that repeated games generate a great diversity of behavioral equilibria, in support of the norm psychology hypothesis’s premise. When interaction is repeated, adopting local norms is a more evolutionarily successful strategy than automatically cooperating. If various groups are at different behavioral equilibria, then cultural selection between groups tends to select for cooperative behavior.
Zr-based coating for the prevention of silver tarnishing
Authors: Stoulil Jan , Anisová Martina , Mistova Eva , Fojt Jaroslav 
Published: December 2013

Purpose
– This work aims to focus on evaluation of the ability of cathodically deposited ZrO2-based coatings to stabilise the surface of silver against tarnishing caused by S2−-based species and comparison of these coatings with Cr oxide-based coating.

Design/methodology/approach
– The coatings were evaluated using inductively coupled plasma optical emission spectroscopy (ICP-OES), scanning electron microscopy (SEM), impedance spectroscopy (EIS) and galvanostatic reduction of specimens exposed to H2S vapours.

Findings
– The kinetics of deposition were studied and optimum conditions for coating formation were determined. The options of manual application suitable for practical use were studied also. Zr specimens showed better barrier properties than did a chromated specimen. The best properties were observed on a specimen with a manually fast-applied coating. However, Zr coating does not provide as good protection from tarnishing as chromate. The structure of the Cr coating contains species of chromate that oxidize species of S2−.

Originality/value
– The paper provides new information regarding the anticorrosive properties of cathodically deposited ZrO2 coating as an alternative to Cr coating for the preservation of silver surfaces.
Related party transactions and separation between control and direction in business groups: the Italian case
Authors: Di Carlo Emiliano 
Published: December 2013

Purpose–Under IAS 24 a related party transaction (RPT) is a “transfer of resources, services or obligations between related parties, regardless of whether a price is charged” (IASB). The purpose of this paper is to consider the interest of the business group and the directing activity of the parent company for the interpretation of the RPT. Considering the interest of the group means to interpret the intra-group transactions not as isolated transactions, as usually done by the empirical studies, but in a wider perspective, that of the group.Design/methodology/approach–This paper builds on explanatory multiple case studies in order to answer the following research questions: why the interest of the business group and the directing activity of the subsidiaries by the parent company are important in the interpretation of RPTs. How RPTs can be interpreted in the light of the directing activity of the holding company.Findings–Dominant shareholder tends to demonstrate that the group it is not managed as a single economic entity and sometimes that subsidiaries are not really controlled. The case studies show that a regulation that imposes the transparency of the directing activity has at least two effects: the controlling shareholder finds it convenient to delegate the decision-making power and to not carry out RPTs among firms that do not present clear economic links. Thus, the transparency of the directing activity seems to be a disincentive to the establishment of a pyramidal group with expropriation purposes.Research limitations/implications–It is appropriate that the interpretation of the RPT take into account not only the disclosure of the RPT (e.g. type and nature), but also the following disclosure: the reason and the business purpose that lead to RPT; the interest of the company in engaging such transactions; and the procedures for their approval. The independence of subsidiaries directors is necessary to ensure the management autonomy of the boards, and in the case of directing activity they have to protect outsiders in the case of detrimental transactions ordered by the controlling and directing company that are not carried out in the interest of the group.Originality/value–Unlike what has been done so far by the literature on RPT, this paper considers the interest of the group to interpret the intra-group transactions and the separation between control and direction. It means do not interpret RPT as isolated transactions, as usually done by the empirical studies, but in a wider perspective, that of the group.
CGIJ review
Authors: MacVane Phipps Fiona 
Published: December 2013

Purpose
– The purpose of this review is to enable readers of the journal to gain a quick over-view of articles published in this issue.

Design/methodology/approach
– A review of articles published within this issue of CGIJ with added commentary.

Findings
– Clinical governance continues to be an important issue in contemporary healthcare and the concept is being applied to many different facets of healthcare provision.

Originality/value
– The originality value is that CGIJ is the only Emerald journal containing this type of review section.
Modelling of a desiccant rotor by using the collocation method
Authors: Aprile Marcello , Motta Mario 
Published: December 2013

Purpose
– This article aims to develop a fast numerical method for solving the one-dimensional heat and mass transfer problem within a desiccant rotor.

Design/methodology/approach
– The collocation method is used for discretizing the axial dimension and reducing the number of dependent variables. The resulting system of equation is then solved through backward differentiation formulas.

Findings
– The numerical results obtained here focus on verifying the accuracy and the computation time of the proposed method with respect to the finite difference method. The proposed numerical solution method resulted faster than, and as much accurate as, the finite difference method, over a large range of operating conditions that are of interest in desiccant cooling applications.

Research limitations/implications
– For heat and mass transfer analysis, constant average transfer coefficients are used. The results are calculated for NTU between 2 and 15 and for Le number between 0.5 and 2.

Practical implications
– The results can be used in designing desiccant heat exchangers and desiccant cooling systems including complex rotor arrangements.

Originality/value
– Different from other simplified solution techniques, the proposed method relies on few parameters that retain physical meaning and applies also to complex rotor configurations.
Simulation of turbulent duct flow by employing shear-improved Smagorinsky model accompanied by forced generalized lattice Boltzmann method
Authors: Jafari S. , Rahnama M. , Jahanshahi Javaran E. 
Published: December 2013

Purpose– The present work aims to deal with simulation of turbulent duct flow using generalized lattice Boltzmann equation (GLBE) in which large eddy simulation was employed.Design/methodology/approach– The sub-grid scale turbulence effects were simulated through a shear-improved Smagorinsky model (SISM) which is capable of predicting turbulent near wall region accurately without any wall function. Computations were done for fully developed turbulent square duct flow at Ret=300, based on duct width and average friction velocity.Findings– Results obtained for turbulent duct flow reveal that the GLBE in conjunction with SISM is able to correctly predict the existence of secondary flows and the computed detailed structure of first- and second-order statistics of main and secondary motions. The methodology is validated by comparing with previously published data. It is concluded that such framework is capable of predicting accurate results for turbulent duct flow. In addition, the operations in the present method are local; it can be easily programmed for parallel machines.Originality/value– The numerical method, including generalized lattice Boltzmann method with forcing term and implementation of SISM in GLBE, is used for the first time to simulate turbulent duct flow.
Coupled magneto-buoyant convection and radiation in an inclined enclosure
Authors: K. Jena Sofen , K. Mahapatra Swarup , Sarkar Amitava 
Published: December 2013

Purpose
– The current study aims to address the interaction between participating media radiation with thermo-gravitational convection of an electrically conducting fluid enclosed within a tilted enclosure under an externally imposed time-independent uniform magnetic field.

Design/methodology/approach
– The differentially heated boundaries of the tilted enclosure are considered to be diffuse, gray and the enclosed fluid is assumed to be absorbing, emitting and isotropically scattering. The Navier-Stokes equations, meant for magneto convection are solved using modified MAC method. Gradient dependent consistent hybrid upwind scheme of second order is used for discretization of the convective terms. Discrete ordinate method, with S8 approximation, is used to model radiative transport equation in the presence of radiatively active medium.

Findings
– Effect of uniform magnetic field with different magnitudes and orientations of cavity has been numerically simulated. The effect of participating media radiation has been investigated for different optical thicknesses, emissivities, scattering albedos and Planks number. The results are provided in both graphical and tabular forms. The flow lines, isotherms bring clarity in the understanding of flow behaviour and heat transfer characteristics.

Originality/value
– Despite the idealized nature, the present study is quite essential to understand the cumbersome physics of realistic problem.
Linking core self-evaluations and work engagement to work-family facilitation
Authors: M. Karatepe Osman , Demir Eda 
Published: December 2013

Purpose
– This article aims to develop and test a research model that investigates work engagement as a mediator of the effect of core self-evaluations on work-family facilitation and family-work facilitation.

Design/methodology/approach
– The relationships were tested via structural equation modeling using data collected from a sample of full-time frontline hotel employees with a time lag of two weeks in Turkey.

Findings
– The results suggest that work engagement functions as a full mediator of the impact of core self-evaluations on work-family facilitation and family-work facilitation. Specifically, frontline employees with positive core self-evaluations are highly engaged in their work, and therefore, are capable of integrating their work (family) and family (work) roles successfully.

Practical implications
– Management of the hotels can utilize the core self-evaluations scale to hire the right person in frontline service jobs. They should invest in high-performance work practices (i.e. training and re-training, empowerment, rewards, job security, career opportunities) simultaneously for retention of employees with positive core self-evaluations. When such employees learn that the organization implements these practices due to management commitment to delivery of service quality and retention of employees, they are highly engaged in their work. The presence of a family-supportive work environment would also enable managers to retain these frontline employees.

Originality/value
– This study expands current knowledge by assessing work engagement as a mediator of the impact of core self-evaluations on work-family facilitation and family-work facilitation.
Toward an integrated model of adoption of mobile phones for purchasing ancillary services in air travel
Authors: Morosan Cristian 
Published: December 2013

Purpose
– Recently, ancillary services' (e.g. bag processing, preferred seating) contribution to the overall air travel revenues has become substantial. Yet, no study to date has addressed how these services are purchased. This study aims to investigate air travelers' adoption of mobile phones to purchase ancillary air travel services.

Design/methodology/approach
– A comprehensive structural model was developed based on the Technology Acceptance Model and augmented with constructs like trust, privacy, security, innovativeness, and personalization. The model was validated using confirmatory factor analysis and structural equations modeling.

Findings
– The model explained 84 percent of the variability in intentions to use mobile phones to purchase air travel ancillary services. The strongest predictor of attitudes was perceived usefulness, followed by perceived ease of use and trust.

Research limitations/implications
– First, this study's extended theoretical framework was well supported, as it captures relevant system perceptions (e.g. usefulness, ease of use) and personal traits of consumers (e.g. innovativeness), thus extending the classic paradigmatic approach to technology adoption beyond system beliefs. Second, the study explains the relationships among trust, security, and privacy in m-commerce. Third, this study explicates the roles of innovativeness and personalization, which have not been examined in the context of m-commerce in travel.

Practical implications
– This study offers managers an understanding of factors leading to adoption of mobile phones for purchasing air travel ancillary services.

Originality/value
– This study provides a first theoretical perspective on the purchasing behavior of services that have not been studied so far, but have an increasingly substantial financial significance for the airline industry.