bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein complex prediction based on simultaneous protein interaction network
Authors: Jung Suk Hoon , Hyun Bora , Jang Woo-Hyuk , Hur Hee-Young , Han Dong-Soo 
Published: December 2009

Abstract
Motivation: The increase in the amount of available protein–protein interaction (PPI) data enables us to develop computational methods for protein complex predictions. A protein complex is a group of proteins that interact with each other at the same time and place. The protein complex generally corresponds to a cluster in PPI network (PPIN). However, clusters correspond not only to protein complexes but also to sets of proteins that interact dynamically with each other. As a result, conventional graph-theoretic clustering methods that disregard interaction dynamics show high false positive rates in protein complex predictions.
Results: In this article, a method of refining PPIN is proposed that uses the structural interface data of protein pairs for protein complex predictions. A simultaneous protein interaction network (SPIN) is introduced to specify mutually exclusive interactions (MEIs) as indicated from the overlapping interfaces and to exclude competition from MEIs that arise during the detection of protein complexes. After constructing SPINs, naive clustering algorithms are applied to the SPINs for protein complex predictions. The evaluation results show that the proposed method outperforms the simple PPIN-based method in terms of removing false positive proteins in the formation of complexes. This shows that excluding competition between MEIs can be effective for improving prediction accuracy in general computational approaches involving protein interactions.
Availability: http://code.google.com/p/simultaneous-pin/
Contact: dshan@kaist.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
Biomarker detection in the integration of multiple multi-class genomic studies
Authors: Lu Shuya , Li Jia , Song Chi , Shen Kui , Tseng George C. 
Published: December 2009

Abstract
Motivation: Systematic information integration of multiple-related microarray studies has become an important issue as the technology becomes mature and prevalent in the past decade. The aggregated information provides more robust and accurate biomarker detection. So far, published meta-analysis methods for this purpose mostly consider two-class comparison. Methods for combining multi-class studies and considering expression pattern concordance are rarely explored.
Results: In this article, we develop three integration methods for biomarker detection in multiple multi-class microarray studies: ANOVA-maxP, min-MCC and OW-min-MCC. We first consider a natural extension of combining P-values from the traditional ANOVA model. Since P-values from ANOVA do not guarantee to reflect the concordant expression pattern information across studies, we propose a multi-class correlation (MCC) measure to specifically seek for biomarkers of concordant inter-class patterns across a pair of studies. For both ANOVA and MCC approaches, we use extreme order statistics to identify biomarkers differentially expressed (DE) in all studies (i.e. ANOVA-maxP and min-MCC). The min-MCC method is further extended to identify biomarkers DE in partial studies by incorporating a recently developed optimally weighted (OW) technique (OW-min-MCC). All methods are evaluated by simulation studies and by three meta-analysis applications to multi-tissue mouse metabolism datasets, multi-condition mouse trauma datasets and multi-malignant-condition human prostate cancer datasets. The results show complementary strength of the three methods for different biological purposes.
Availability: http://www.biostat.pitt.edu/bioinfo/
Contact: ctseng@pitt.edu
Supplementary information: Supplementary data is available at Bioinformatics online.
Relating marine ecosystem indicators to fishing and environmental drivers: an elucidation of contrasting responses
Authors: Link Jason S. , Yemane Dawit , Shannon Lynne J. , Coll Marta , Shin Yunne-Jai , Hill Louize , Borges Maria de Fatima 
Published: December 2009

Abstract
Link, J. S., Yemane, D., Shannon, L. J., Coll, M., Shin, Y-J., Hill, L., and Borges, M. F. 2010. Relating marine ecosystem indicators to fishing and environmental drivers: an elucidation of contrasting responses. – ICES Journal of Marine Science, 67: 787–795. The usefulness of indicators in detecting ecosystem change depends on three main criteria: the availability of data to estimate the indicator (measurability), the ability to detect change in an ecosystem (sensitivity), and the ability to link the said change in an indicator as a response to a known intervention or pressure (specificity). Here, we specifically examine the third aspect of indicator change, with an emphasis on multiple methods to explore the “relativity” of major ecosystem drivers. We use a suite of multivariate methods to explore the relationships between a pre-established set of fisheries-orientated ecosystem status indicators and the key drivers for those ecosystems (particularly emphasizing proxy indicators for fishing and the environment). The results show the relative importance among fishing and environmental factors, which differed notably across the major types of ecosystems. Yet, they also demonstrated common patterns in which most ecosystems, and indicators of ecosystem dynamics are largely driven by fisheries (landings) or human (human development index) factors, and secondarily by environmental drivers (e.g. AMO, PDO, SST). How one might utilize this empirical evidence in future efforts for ecosystem approaches to fisheries is discussed, highlighting the need to manage fisheries in the context of environmental and other human (e.g. economic) drivers.
Tracing Cationic Nutrients from Xylem into Stem Tissue of French Bean by Stable Isotope Tracers and Cryo-Secondary Ion Mass Spectrometry
Authors: Metzner Ralf , Schneider Heike Ursula , Breuer Uwe , Thorpe Michael Robert , Schurr Ulrich , Schroeder Walter Heinz 
Published: December 2009

Abstract
Fluxes of mineral nutrients in the xylem are strongly influenced by interactions with the surrounding stem tissues and are probably regulated by them. Toward a mechanistic understanding of these interactions, we applied stable isotope tracers of magnesium, potassium, and calcium continuously to the transpiration stream of cut bean (Phaseolus vulgaris) shoots to study their radial exchange at the cell and tissue level with stem tissues between pith and phloem. For isotope localization, we combined sample preparation with secondary ion mass spectrometry in a completely cryogenic workflow. After 20 min of application, tracers were readily detectable to various degrees in all tissues. The xylem parenchyma near the vessels exchanged freely with the vessels, its nutrient elements reaching a steady state of strong exchange with elements in the vessels within 20 min, mainly via apoplastic pathways. A slow exchange between vessels and cambium and phloem suggested that they are separated from the xylem, parenchyma, and pith, possibly by an apoplastic barrier to diffusion for nutrients (as for carbohydrates). There was little difference in these distributions when tracers were applied directly to intact xylem via a microcapillary, suggesting that xylem tension had little effect on radial exchange of these nutrients and that their movement was mainly diffusive.
Real-Time Imaging of Cellulose Reorientation during Cell Wall Expansion in Arabidopsis Roots
Authors: Anderson Charles T. , Carroll Andrew , Akhmetova Laila , Somerville Chris 
Published: December 2009

Abstract
Cellulose forms the major load-bearing network of the plant cell wall, which simultaneously protects the cell and directs its growth. Although the process of cellulose synthesis has been observed, little is known about the behavior of cellulose in the wall after synthesis. Using Pontamine Fast Scarlet 4B, a dye that fluoresces preferentially in the presence of cellulose and has excitation and emission wavelengths suitable for confocal microscopy, we imaged the architecture and dynamics of cellulose in the cell walls of expanding root cells. We found that cellulose exists in Arabidopsis (Arabidopsis thaliana) cell walls in large fibrillar bundles that vary in orientation. During anisotropic wall expansion in wild-type plants, we observed that these cellulose bundles rotate in a transverse to longitudinal direction. We also found that cellulose organization is significantly altered in mutants lacking either a cellulose synthase subunit or two xyloglucan xylosyltransferase isoforms. Our results support a model in which cellulose is deposited transversely to accommodate longitudinal cell expansion and reoriented during expansion to generate a cell wall that is fortified against strain from any direction.
Thylakoid Protein Phosphorylation in Higher Plant Chloroplasts Optimizes Electron Transfer under Fluctuating Light
Authors: Tikkanen Mikko , Grieco Michele , Kangasjaݶrvi Saijaliisa , Aro Eva-Mari 
Published: December 2009

AbstractSeveral proteins of photosystem II (PSII) and its light-harvesting antenna (LHCII) are reversibly phosphorylated according to light quantity and quality. Nevertheless, the interdependence of protein phosphorylation, nonphotochemical quenching, and efficiency of electron transfer in the thylakoid membrane has remained elusive. These questions were addressed by investigating in parallel the wild type and the stn7, stn8, and stn7 stn8 kinase mutants of Arabidopsis (Arabidopsis thaliana), using the stn7 npq4, npq4, npq1, and pgr5 mutants as controls. Phosphorylation of PSII-LHCII proteins is strongly and dynamically regulated according to white light intensity. Yet, the changes in phosphorylation do not notably modify the relative excitation energy distribution between PSII and PSI, as typically occurs when phosphorylation is induced by “state 2” light that selectively excites PSII and induces the phosphorylation of both the PSII core and LHCII proteins. On the contrary, under low-light conditions, when excitation energy transfer from LHCII to reaction centers is efficient, the STN7-dependent LHCII protein phosphorylation guarantees a balanced distribution of excitation energy to both photosystems. The importance of this regulation diminishes at high light upon induction of thermal dissipation of excitation energy. Lack of the STN7 kinase, and thus the capacity for equal distribution of excitation energy to PSII and PSI, causes relative overexcitation of PSII under low light but not under high light, leading to disturbed maintenance of fluent electron flow under fluctuating light intensities. The physiological relevance of the STN7-dependent regulation is evidenced by severely stunted phenotypes of the stn7 and stn7 stn8 mutants under strongly fluctuating light conditions.
Reactive Oxygen Species Are Involved in Plant Defense against a Gall Midge
Authors: Liu Xuming , Williams Christie E. , Nemacheck Jill A. , Wang Haiyan , Subramanyam Subhashree , Zheng Cheng , Chen Ming-Shun 
Published: December 2009

AbstractReactive oxygen species (ROS) play a major role in plant defense against pathogens, but evidence for their role in defense against insects is still preliminary and inconsistent. In this study, we examined the potential role of ROS in defense of wheat (Triticum aestivum) and rice (Oryza sativa) against Hessian fly (Mayetiola destructor) larvae. Rapid and prolonged accumulation of hydrogen peroxide (H2O2) was detected in wheat plants at the attack site during incompatible interactions. Increased accumulation of both H2O2 and superoxide was detected in rice plants during nonhost interactions with the larvae. No increase in accumulation of either H2O2 or superoxide was observed in wheat plants during compatible interactions. A global analysis revealed changes in the abundances of 250 wheat transcripts and 320 rice transcripts encoding proteins potentially involved in ROS homeostasis. A large number of transcripts encoded class III peroxidases that increased in abundance during both incompatible and nonhost interactions, whereas the levels of these transcripts decreased in susceptible wheat during compatible interactions. The higher levels of class III peroxidase transcripts were associated with elevated enzymatic activity of peroxidases at the attack site in plants during incompatible and nonhost interactions. Overall, our data indicate that class III peroxidases may play a role in ROS generation in resistant wheat and nonhost rice plants during response to Hessian fly attacks.
A Root-Expressed Magnesium Transporter of theMRS2/MGTGene Family inArabidopsis thalianaAllows for Growth in Low-Mg2+ Environments
Authors: Gebert Michael , Meschenmoser Karoline , Svidová Soňa , Weghuber Julian , Schweyen Rudolf , Eifler Karolin , Lenz Henning , Weyand Katrin , Knoop Volker 
Published: December 2009

AbstractThe MRS2/MGT gene family in Arabidopsis thaliana belongs to the superfamily of CorA-MRS2-ALR-type membrane proteins. Proteins of this type are characterized by a GMN tripeptide motif (Gly-Met-Asn) at the end of the first of two C-terminal transmembrane domains and have been characterized as magnesium transporters. Using the recently established mag-fura-2 system allowing direct measurement of Mg2+ uptake into mitochondria of Saccharomyces cerevisiae, we find that all members of the Arabidopsis family complement the corresponding yeast mrs2 mutant. Highly different patterns of tissue-specific expression were observed for the MRS2/MGT family members in planta. Six of them are expressed in root tissues, indicating a possible involvement in plant magnesium supply and distribution after uptake from the soil substrate. Homozygous T-DNA insertion knockout lines were obtained for four members of the MRS2/MGT gene family. A strong, magnesium-dependent phenotype of growth retardation was found for mrs2-7 when Mg2+ concentrations were lowered to 50 μM in hydroponic cultures. Ectopic overexpression of MRS2-7 from the cauliflower mosaic virus 35S promoter results in complementation and increased biomass accumulation. Green fluorescent protein reporter gene fusions indicate a location of MRS2-7 in the endomembrane system. Hence, contrary to what is frequently found in analyses of plant gene families, a single gene family member knockout results in a strong, environmentally dependent phenotype.
UK industrial relations state agencies
Authors: Gennard John 
Published: December 2009

PurposeThe purpose of this Editorial is to outline the main functions of the UK industrial relations state agencies – the Certification Officer, the Central Arbitration Committee and The Advisory Conciliation and Arbitration Service.Design/methodology/approachThe Editorial outlines the main functions of the UK industrial relations state agencies, explaining their history and roles.FindingsThe Editorial reveals detailed information about the main functions of the UK industrial relations state agencies.Originality/valueThe Editorial offers insights into the work of UK industrial relations state agencies.
The roles and functions of shop stewards in workplace partnership
Authors: Rittau Yasmin , Dundon Tony 
Published: December 2009

PurposeThe purpose of this paper is to examine the roles and influence of shop stewards under workplace partnership regimes in five case study firms in the Republic of Ireland. It aims to assess the dynamics and potential longevity of partnership relationships.Design/methodology/approachA framework is utilised which analyses the scope, breadth and depth of union influence in terms of the structure of partnership processes and the capacity of agency to affect relations among shop stewards, union members and plant management.FindingsThe findings show that while union representatives view partnership in a positive light, there remain problems as to the longevity of partnership owing to management control and a disconnection between national (government) and local (workplace) support mechanisms for partnership. The paper concludes that social partnership is a process that remains anchored in a relationship of both antagonism and accommodation between capital and labour.Originality/valueMuch of the extant literature tends to focus on the outcomes of partnership in terms of the gains or losses to either management and/or unions. In this paper, the focus is on the way the “processes” of social partnership shape the behaviour and roles of workplace union representatives. A number of theoretical and policy implications are discussed.
Employees' attitudes towards diversity in a non‐western context
Authors: Alserhan Bakr Ahmad , Forstenlechner Ingo , Al‐Nakeeb Ahmad 
Published: December 2009

PurposeThe purpose of this paper is to examine attitudes towards diversity in an emerging Gulf economy whose workforce is dominated by expatriates and is under significant pressure to accommodate host country citizens. It seeks to examine employees' attitudes towards workforce diversity in the banking sector in the United Arab Emirates (UAE).Design/methodology/approachA total of 100 employees from 11 banks are chosen randomly from banks operating in the UAE. Those employees are asked to answer a questionnaire containing various questions that cover the applauded benefits of diversity as identified in the related literature.FindingsAll banks have a diverse workforce, with nationals representing a minority in all of them. However, banks differ on the various indicators of diversity with some being more religiously diverse while others more diverse in terms of nationalities or languages. Overall, Islamic banks are the least diverse on all dimensions of diversity.Research limitations/implicationsSeveral obstacles are faced during the course of this study including limitations on access to employees, sampling limitations preventing more in‐depth analysis of certain aspects, lack of regional studies on diversity and the timing of the survey itself which coincide with the summer exodus of expatriates.Originality/valueThis paper provides useful information on attitudes toward diversity in an emerging Gulf economy, dominated by expatriates.
The changing nature of the traditional expatriate psychological contract
Authors: Pate Judy , Scullion Hugh 
Published: December 2009

PurposeThe purpose of this paper is to examine whether traditional conventions of the expatriate psychological contract have altered from both employer and employee perspectives. In essence to what extent have multi‐national corporations adjusted organisational practices to reflect changing circumstances and to what extent have expatriates altered their mindset towards employers' obligations and requirements.Design/methodology/approachThe paper draws on findings of three organisational case studies and is based on in‐depth interviews with HR managers, line managers and expatriates.FindingsThe findings reveale that the overall tone of the psychological contract from the employers' perspective is transactional. From an employee perspective, preliminary evidence suggests that the dynamics of the employment relationship is changing and that employees have responded to contract changes by seeking to ensure their employability and reduce their dependence on a single organisation.Practical implicationsThe paper focuses on four areas for managers: first, pro‐actively influencing expatriates' expectations thereby minimising misunderstandings; second, organisations should be very aware of “the remuneration market rate” for a particular location; third, policies of support and contact would aid feelings of integration. Finally, more attention should be paid new approaches to strategic talent management.Originality/valueThis paper contributes theoretically and empirically to the literature on expatriates' psychological contracts, an area where there is a dearth of empirical research. The paper also increases the understanding of the variety of expatriate perceptions in different contexts, thereby deepening the understanding of the importance of context in this area.
How much would US union membership increase under a policy of non‐exclusive representation?
Authors: Harcourt Mark , Lam Helen 
Published: December 2009

PurposeIn light of the low‐union density and a huge representation gap in the US representation system. The purpose of this paper is to examine the effectiveness of the system under majority rule and to provide some empirical evidence on how much union membership would increase in the USA if a policy of non‐exclusive representation, as adopted in New Zealand, are to be implemented.Design/methodology/approachThe sample for the study consists of 227 New Zealand organizations, employing over 180,000 workers. Logistic regression is used for the analysis with the dichotomous dependent variable indicating whether there is majority union support.FindingsIf the USA allowed and supported minority unionism, union membership could increase by 30 percent or more. Workers in smaller, private‐sector organizations outside healthcare, education, and manufacturing are most disadvantaged by the majority‐rule system.Practical implicationsGiven that many workers' needs for representation have not been addressed by the current US majority rule system, consideration of minority representation to enhance representation effectiveness and understanding its implications are of critical importance, especially for a democratic society.Originality/valueThe paper offers empirical data on the implications of a change of the US representation system and proposes three options for incorporating minority representation.
The use and sharing of information from Wikipedia by high‐tech professionals for work purposes
Authors: Chen Hsin‐liang 
Published: December 2009

PurposeThe aim of this paper is to focus on discovering whether high‐tech professionals as a user community search for information from Wikipedia to fulfill their job duties and, if they do, how they share information with co‐workers and clients.Design/methodology/approachAn online questionnaire was used, administered by a commercial provider. The questionnaire consisted of 15 Likert‐scaled questions to assess participants' agreement with each question along with an optional open‐ended explanation. A total of 68 participants successfully answered the questionnaire. Participants' Likert rating scores were analyzed by two‐way ANOVA, one‐way ANOVA and correlational analyses using SPSS.FindingsThe analyses examined relationships among participants' characteristics, their use of information resources for research and teaching, information‐sharing behaviors, and use/non‐use of Wikipedia. Findings indicated that the participants treated Wikipedia as a ready reference for general information. Their concern is that Wikipedia only has a limited number of entries available at this point. They suggested that Wikipedia needed to improve the contribution and editorial process and to make it more rigorous.Originality/valuePersonal information infrastructure affects how the high‐tech professionals surveyed use‐and‐share information from Wikipedia for work. In the current situation, the participants consider Wikipedia to be a developing information resource and show less interest in contributing to it. The project is an exploratory study and more considerations are needed for this research area.