bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graphene patterned polyaniline-based biosensor for glucose detection
Authors: Nguyen Hai Binh , Nguyen Van Chuc , Nguyen Van Tu , Ngo Thi Thanh Tam , Nguyen Ngoc Thinh , Dang Thi Thu Huyen , Tran Dai Lam , Do Phuc Quan , Nguyen Xuan Nghia , Nguyen Xuan Phuc , Phan Hong Khoi , Phan Ngoc Minh 
Published: May 2012

Abstract
This paper describes a glucose electrochemical biosensor, layer-by-layer fabricated from graphene and polyaniline films. Graphene sheets (0.5×0.5 cm
2) with the thickness of 5 nm (15 layers) were synthesized by thermal chemical vapor deposition (CVD) under ambient pressure on copper tapes. Then they were transferred into integrated Fe
3
O
4-doped polyaniline (PANi) based microelectrodes. The properties of the nanocomposite films were thoroughly characterized by scanning electron microscopy (SEM), Raman spectroscopy, atomic force microscopy (AFM) and electrochemical methods, such as square wave voltametry (SWV) and chronoamperometry. The above graphene patterned sensor (denoted as Graphene/Fe
3
O
4/PANi/GOx) shows much improved glucose sensitivity (as high as 47 μA
mM
−1
cm
−2) compared to a non-graphene one (10–30 μA
mM
−1
cm
−2, as previously reported in the literature). It can be expected that this proof-of-concept biosensor could be extended for other highly sensitive biodetection.
Identifying differentially expressed transcripts from RNA-seq data with biological variation
Authors: Glaus Peter , Honkela Antti , Rattray Magnus 
Published: May 2012

Abstract
Motivation: High-throughput sequencing enables expression analysis at the level of individual transcripts. The analysis of transcriptome expression levels and differential expression (DE) estimation requires a probabilistic approach to properly account for ambiguity caused by shared exons and finite read sampling as well as the intrinsic biological variance of transcript expression.
Results: We present Bayesian inference of transcripts from sequencing data (BitSeq), a Bayesian approach for estimation of transcript expression level from RNA-seq experiments. Inferred relative expression is represented by Markov chain Monte Carlo samples from the posterior probability distribution of a generative model of the read data. We propose a novel method for DE analysis across replicates which propagates uncertainty from the sample-level model while modelling biological variance using an expression-level-dependent prior. We demonstrate the advantages of our method using simulated data as well as an RNA-seq dataset with technical and biological replication for both studied conditions.
Availability: The implementation of the transcriptome expression estimation and differential expression analysis, BitSeq, has been written in C++ and Python. The software is available online from http://code.google.com/p/bitseq/, version 0.4 was used for generating results presented in this article.
Contact: glaus@cs.man.ac.uk, antti.honkela@hiit.fi or m.rattray@sheffield.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
SEQCHIP: a powerful method to integrate sequence and genotype data for the detection of rare variant associations
Authors: Liu Dajiang J. , Leal Suzanne M. 
Published: May 2012

Abstract
Motivation: Next-generation sequencing greatly increases the capacity to detect rare-variant complex-trait associations. However, it is still expensive to sequence a large number of samples and therefore often small datasets are used. Given cost constraints, a potentially more powerful two-step strategy is to sequence a subset of the sample to discover variants, and genotype the identified variants in the remaining sample. If only cases are sequenced, directly combining sequence and genotype data will lead to inflated type-I errors in rare-variant association analysis. Although several methods have been developed to correct for the bias, they are either underpowered or theoretically invalid. We proposed a new method SEQCHIP to integrate genotype and sequence data, which can be used with most existing rare-variant tests.
Results: It is demonstrated using both simulated and real datasets that the SEQCHIP method has controlled type-I errors, and is substantially more powerful than all other currently available methods.
Availability: SEQCHIP is implemented in an R-Package and is available at http://linkage.rockefeller.edu/suzanne/seqchip/Seqchip.htm
Contacts: dajiang@umich.edu or sleal@bcm.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Trends of fish and elasmobranch landings in Italy: associated management implications
Authors: Dell'Apa Andrea , Kimmel David G. , Clò Simona 
Published: May 2012

AbstractDell'Apa, A., Kimmel, D. G., and Clò, S. 2012. Trends of fish and elasmobranch landings in Italy: associated management implications. – ICES Journal of Marine Science, 69: 1045–1052. Elasmobranchs are extremely vulnerable to overexploitation, owing to their specific biology and life-history characteristics. However, European-managed shark fisheries have historically received less attention than fisheries targeting more commercially important fish species. We analysed and compared the national data of elasmobranch and fish landings in Italy between 1959 and 2004 to examine changes in fishery interest and the exploitation of elasmobranchs over time. Rays (Raja spp.) and smooth-hounds (Mustelus spp.) are the only elasmobranch categories present in the data, but also other similar species could have been mistakenly counted within these groups. Elasmobranch landings were steady until the beginning of the 1970s, peaked in the 1990s, then sharply declined. The mean annual landing for elasmobranchs between 1997 and 2004 decreased 77% compared with the previous years (1959–1982). This decrease may be attributed to overharvesting that occurred during the 1980s and 1990s in Italian seas. This was likely a direct consequence of the 41/82-law, which was developed to manage fish and not elasmobranchs. A direct effect of the 41/82-law was the establishment of an unreported and unregulated elasmobranch fishery since 1983 that lasted almost 10 years. We suggest that the conservation status of elasmobranch species in the Mediterranean and Black Seas be reconsidered.
Copper Chaperone Antioxidant Protein1 Is Essential for Copper Homeostasis
Authors: Shin Lung-Jiun , Lo Jing-Chi , Yeh Kuo-Chen 
Published: May 2012

Abstract
Copper (Cu) is essential for plant growth but toxic in excess. Specific molecular mechanisms maintain Cu homeostasis to facilitate its use and avoid the toxicity. Cu chaperones, proteins containing a Cu-binding domain(s), are thought to assist Cu intracellular homeostasis by their Cu-chelating ability. In Arabidopsis (Arabidopsis thaliana), two Cu chaperones, Antioxidant Protein1 (ATX1) and ATX1-Like Copper Chaperone (CCH), share high sequence homology. Previously, their Cu-binding capabilities were demonstrated and interacting molecules were identified. To understand the physiological functions of these two chaperones, we characterized the phenotype of atx1 and cch mutants and the cchatx1 double mutant in Arabidopsis. The shoot and root growth of atx1 and cchatx1 but not cch was specifically hypersensitive to excess Cu but not excess iron, zinc, or cadmium. The activities of antioxidant enzymes in atx1 and cchatx1 were markedly regulated in response to excess Cu, which confirms the phenotype of Cu hypersensitivity. Interestingly, atx1 and cchatx1 were sensitive to Cu deficiency. Overexpression of ATX1 not only enhanced Cu tolerance and accumulation in excess Cu conditions but also tolerance to Cu deficiency. In addition, the Cu-binding motif MXCXXC of ATX1 was required for these physiological functions. ATX1 was previously proposed to be involved in Cu homeostasis by its Cu-binding activity and interaction with the Cu transporter Heavy metal-transporting P-type ATPase5. In this study, we demonstrate that ATX1 plays an essential role in Cu homeostasis in conferring tolerance to excess Cu and Cu deficiency. The possible mechanism is discussed.
Looking Deep Inside: Detection of Low-Abundance Proteins in Leaf Extracts of Arabidopsis and Phloem Exudates of Pumpkin
Authors: Fröhlich Andreas , Gaupels Frank , Sarioglu Hakan , Holzmeister Christian , Spannagl Manuel , Durner Jörg , Lindermayr Christian 
Published: May 2012

Abstract
The field of proteomics suffers from the immense complexity of even small proteomes and the enormous dynamic range of protein concentrations within a given sample. Most protein samples contain a few major proteins, which hamper in-depth proteomic analysis. In the human field, combinatorial hexapeptide ligand libraries (CPLL; such as ProteoMiner) have been used for reduction of the dynamic range of protein concentrations; however, this technique is not established in plant research. In this work, we present the application of CPLL to Arabidopsis (Arabidopsis thaliana) leaf proteins. One- and two-dimensional gel electrophoresis showed a decrease in high-abundance proteins and an enrichment of less abundant proteins in CPLL-treated samples. After optimization of the CPLL protocol, mass spectrometric analyses of leaf extracts led to the identification of 1,192 proteins in control samples and an additional 512 proteins after the application of CPLL. Upon leaf infection with virulent Pseudomonas syringae DC3000, CPLL beads were also used for investigating the bacterial infectome. In total, 312 bacterial proteins could be identified in infected Arabidopsis leaves. Furthermore, phloem exudates of pumpkin (Cucurbita maxima) were analyzed. CPLL prefractionation caused depletion of the major phloem proteins 1 and 2 and improved phloem proteomics, because 67 of 320 identified proteins were detectable only after CPLL treatment. In sum, our results demonstrate that CPLL beads are a time- and cost-effective tool for reducing major proteins, which often interfere with downstream analyses. The concomitant enrichment of less abundant proteins may facilitate a deeper insight into the plant proteome.
The profit impacts of risk management tool adoption
Authors: Kuethe Todd H. , Morehart Mitch 
Published: May 2012

PurposeThe purpose of this paper is to measure the profit impacts of adopting input and output risk management tools at the farm level.Design/methodology/approachThe analysis examines three years of farm‐level data from the Agricultural Resource Management Survey (ARMS) that include detailed questions on the adoption of risk management tools. Propensity score matching is used to control for the endogeneity of adoption decisions, and the profit impacts are estimated based on the matched dataset.FindingsThe adoption of input price risk management tools improves farm‐level profits by 13‐17 percent.Originality/valueThis is the first paper which examines the profit impacts of risk management tools while controlling for the endogeneity of adoption.
Bringing the unemployed back to work in Germany: training programs or wage subsidies?
Authors: Neubäumer Renate 
Published: May 2012

PurposeThe purpose of this paper is to theoretically and empirically investigate the relative effects of wage subsidies and further vocational training on employment prospects.Design/methodology/approachThe paper adopts a theoretical approach that discusses the effects of two major active labor market programs; empirical test using a large administrative data set from Germany and statistical matching techniques.FindingsPreviously subsidized individuals and trained individuals who found a job immediately afterwards have the same employment rates.Practical implicationsFirms value training on a subsidized job as much as formal training programs.Originality/valueThe paper presents a model that draws attention to the role of hiring decisions of firms and to the formation of human capital by training programs and by training on subsidized jobs; estimation of relative average treatment effects on the differentially treated, i.e. participants of two active labor market programs; and comparisons not only of all unemployed but also of unemployed persons taking‐up or keeping a job after program end.
Moral imagination and active imagination: searching in the depths of the psyche
Authors: Rozuel Cécile 
Published: May 2012

PurposeThe purpose of this paper is to highlight the parallels between the ethical concept of moral imagination and the psychoanalytical concept of active imagination. A model combining both concepts is then proposed and discussed. The paper argues that such synthesis is necessary to understand the process of moral deliberation, as well as to foster more consistent moral choices in organisations.Design/methodology/approachThe paper is conceptual, and builds upon relevant literature from the field of business ethics and analytical psychology.FindingsImagination is a thoroughly ambivalent concept, which can be used to pursue moral as well as immoral goals. Moral imagination is an important element influencing decision making, but its quality depends on the state of balance of the psyche. A sound and effective moral imagination must be grounded in a healthy psyche, and needs the assistance of active imagination (or other similar activities) to achieve this. Such inner work is especially necessary for leaders to clarify their moral values and capabilities.Research limitations/implicationsThe Active and Moral Imagination (AMI) model proposed has not been empirically tested; therefore its implications are tentative at this stage. The paper does not discuss in detail other psychological activities which may be complementary to active imagination.Practical implicationsManagers and leaders should reflect on their own unconscious, so as to understand the deeper mechanisms influencing their decisions and behaviours.Originality/valueThe paper presents an interdisciplinary approach to the role of imagination in ethics.
Investigating the value of restorative practice
Authors: Standing Vicky , Fearon Colm , Dee Tim 
Published: May 2012

PurposeIn response to an increasingly high level of exclusion rates for boys within secondary school in the UK, this study seeks to explore the value of restorative practice and justice for changing student behaviour.Design/methodology/approachAs a piece of action research, the authors aimed to look at how methods of restorative practice could work with one student in a secondary school, following a whole school's move towards a personal responsibility charter. The focus of this research remained on the individual male subject, rather than the educational institution. It is based upon a process of reflecting upon key events that happened throughout the study. This research will use qualitative data gained from observing the student at school, as well as interview and written feedback from the subject himself and school staff. The paper is designed to offer real and informative insight into the value of restorative justice and practices.FindingsRestorative practices had little overall impact on improving the subject's behaviour in school. He was able to have a mature discussion with an adult about the behaviour he was demonstrating. Nevertheless, when put back in the classroom situation he was unable to make a conscious decision to alter his negative behaviour. However, his skills in conferencing to resolve conflict were developed through the authors' involvement with him, as well as other school staff, and he was able to understand the school's new charter.Originality/valueThis paper contributes to restorative justice and practice literature and is insightful because of the action research approach taken.
Job satisfaction: factor analysis of Greek primary school principals' perceptions
Authors: Saiti Anna , Fassoulis Konstantinos 
Published: May 2012

PurposeThe purpose of this paper is to investigate the factors that affect the level of job satisfaction that school principals experience and, based on the findings, to suggest policies or techniques for improving it.Design/methodology/approachQuestionnaires were administered to 180 primary school heads in 13 prefectures – one from each of the 13 Greek regions (including the metropolitan area: prefecture of Attiki, Athens) so that the sample would be representative of the whole country. The first section of the questionnaire includes the location of each respondent's school as well as personal and professional characteristics of the primary school teachers, while the second section asked school principals to reply to 36 statements that expressed perceptions relating to their level of job satisfaction. These responses yielded the principal components for factor analysis.FindingsThe results indicate that two factors – the role of superior and school heads' remuneration, and recognition of the principals' efforts – which account for 33.27 per cent of the total sample, seem to be particularly important for school heads' job satisfaction.Research limitations/implicationsThe findings of this study cannot be used to generalize about the whole Greek education system as it only analyzes a small sample. Therefore, analysis of additional data from school principals may be necessary for comparison and to reaffirm the results. Further investigation is also needed in order to isolate the specific elements and significant differences in school heads' satisfaction ratings.Practical implicationsThis paper would be useful to educational planners and policy makers. Meeting the school principals' needs and expectations seems to be a basic component in effective school leadership. As the school principal's role is directly related to human resources management (teachers) and subsequently to child development, the issue of a head's job satisfaction becomes even more pressing.Originality/valueGiven that the existing Greek literature on school management does not contain a substantially detailed discussion specifically on school heads' job satisfaction, this paper may contribute decisively to the smoother and more efficient operation of the school unit.
“How easy can the barley brie”
Authors: Jackson William J. , Paterson Audrey S. , Pong Christopher K.M. , Scarparo Simona 
Published: May 2012

PurposeThis paper seeks to extend the development of the historical accounting research agenda further into the area of popular culture. The work examines the discourses that surrounded the drinking of alcohol in nineteenth century Britain and explores how an accounting failure disrupted the tension between the two established competing discourses, leading to a significant impact on UK drinking culture at the end of the nineteenth century.Design/methodology/approachThe paper employs both primary and secondary sources. Secondary sources are used to develop the main themes of the discourses deployed by the temperance societies and the whisky companies. Primary sources derived from the contemporary press are employed, as necessary, in support.FindingsThe paper demonstrates that accounting, although it may not be central to a discourse or other social structure, can still have a profound impact upon cultural practices. The potential for research into culture and accounting should not therefore be dismissed if no immediate or concrete relationship between culture and accounting can be determined. Further support is provided for studies that seek to expand the accounting research agenda into new territories.Originality/valueThe study of popular culture is relatively novel in accounting research. This paper seeks to add to this research by exploring an area of cultural activity that has hitherto been neglected by researchers, i.e. by exploring how an accounting incident impacted upon the historical consumption of Scotch whisky in the UK.
Improving value chain flexibility and adaptability in build-to-order environments
Authors: Engelhardt-Nowitzki Corinna 
Published: May 2012

Purpose
– Given volatile markets, the ability to quickly act is fundamental for companies – in regard to the internal production and to external supply flows in the value network. Related flexibility and adaptability concepts are vague and contradictory. Managerial methods either imply a generic application level or a narrow focus. Thus, the purpose of this paper is to develop a three-step approach to facilitate a well-directed flexibility and adaptability design within a build-to-order context: context-specific operationalization, thorough segmentation using advanced logistic criteria and purposeful deduction of improvement means.

Design/methodology/approach
– Based on a thorough literature review, a procedural approach is developed and applied within two rigorously conducted company-cases. A triangulation setting is used within the empirical analysis.

Findings
– A company's capability to act appropriately, quickly and economically in the face of volatility can be remarkably advanced through context-specific analysis and well-reasoned segmentation. A respective approach to enhance flexibility and adaptability has to regard rational, emotional and cultural aspects.

Research limitations/implications
– The literature review is selective, not exhaustive. Two case studies cannot cover all thinkable aspects.

Practical implications
– The findings illustrate how flexibility and adaptability measures can be designed purposefully within a company-specific approach. Two potential directions of impact – uncertainty reduction and flexibility/adaptability improvement – are consolidated into significant criteria and applied to thoroughly classified areas in a feasible way.

Originality/value
– Current approaches do not apply a company-specific operationalization approach and are not based on segmentation or are using limited criteria. Besides, most approaches are neither designed for quick operationalization nor continuous application.
Revenue management in road-based freight transportation
Authors: Schönberger Jörn , Kopfer Herbert 
Published: May 2012

Purpose
– Freight carriers operating in a spot-market environment are faced with uncertain future capacity demand, actual revenues, and properties of freight items. They require information about the expected future consumption of limited capacity to derive suitable request acceptance decisions. The purpose of this paper is to present a new idea to improve the handling of inaccurate information on the weight and volume of upcoming requests.

Design/methodology/approach
– The authors start with the definition of a new mathematical optimization model as the backbone of a capacity control system. This model is embedded within a rolling-horizon decision-making process involving consecutively arriving requests. Computational simulation experiments are carried out to evaluate the applicability and efficiency of the proposed decision support system. The authors investigate how the new model contributes towards keeping the negative impacts of inadequate forecasts of the expected volume of future requests as low as possible.

Findings
– In traditional application fields of capacity control (airline ticketing or hotel reservations) the physical extent of a request is always 1 (set/bed/room). In road-based freight transportation the variety of the physical extent of requests is much more complicated and complex. The major finding is that existing capacity control approaches are unable to meet the special requirements of road-haulage. Innovative capacity control features are necessary in order to cope with the higher request portfolio complexity.

Originality/value
– This paper addresses the requirements of a capacity control system for road-based freight transportation. An innovative decision support system is evaluated. For the first time, the authors present a comprehensive quantitative simulation study dedicated to this complicated decision-making situation.