bluuebunny/crossref_metadata_2025_split huggingface dataset:
Treephyler: fast taxonomic profiling of metagenomes
Authors: Schreiber Fabian , Gumrich Peter , Daniel Rolf , Meinicke Peter 
Published: February 2010

Abstract
Summary: Assessment of phylogenetic diversity is a key element to the analysis of microbial communities. Tools are needed to handle next-generation sequencing data and to cope with the computational complexity of large-scale studies. Here, we present Treephyler, a tool for fast taxonomic profiling of metagenomes. Treephyler was evaluated on real metagenome to assess its performance in comparison to previous approaches for taxonomic profiling. Results indicate that Treephyler is in terms of speed and accuracy prepared for next-generation sequencing techniques and large-scale analysis.
Availability: Treephyler is implemented in Perl; it is portable to all platforms and applicable to both nucleotide and protein input data. Treephyler is freely available for download at http://www.gobics.de/fabian/treephyler.php
Contact: fschrei@gwdg.de
A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems
Authors: Qu Lei , Peng Hanchuan 
Published: February 2010

Abstract
Motivation: The fruit fly (Drosophila melanogaster) is a commonly used model organism in biology. We are currently building a 3D digital atlas of the fruit fly larval nervous system (LNS) based on a large collection of fly larva GAL4 lines, each of which targets a subset of neurons. To achieve such a goal, we need to automatically align a number of high-resolution confocal image stacks of these GAL4 lines. One commonly employed strategy in image pattern registration is to first globally align images using an affine transform, followed by local non-linear warping. Unfortunately, the spatially articulated and often twisted LNS makes it difficult to globally align the images directly using the affine method. In a parallel project to build a 3D digital map of the adult fly ventral nerve cord (VNC), we are confronted with a similar problem.
Results: We proposed to standardize a larval image by best aligning its principal skeleton (PS), and thus used this method as an alternative of the usually considered affine alignment. The PS of a shape was defined as a series of connected polylines that spans the entire shape as broadly as possible, but with the shortest overall length. We developed an automatic PS detection algorithm to robustly detect the PS from an image. Then for a pair of larval images, we designed an automatic image registration method to align their PSs and the entire images simultaneously. Our experimental results on both simulated images and real datasets showed that our method does not only produce satisfactory results for real confocal larval images, but also perform robustly and consistently when there is a lot of noise in the data. We also applied this method successfully to confocal images of some other patterns such as the adult fruit fly VNC and center brain, which have more complicated PS. This demonstrates the flexibility and extensibility of our method.
Availability: The supplementary movies, full size figures, test data, software, and tutorial on the software can be downloaded freely from our website http://penglab.janelia.org/proj/principal_skeleton
Contact: pengh@janelia.hhmi.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Comment on “Purported flaws in management strategy evaluation: basic problems or misinterpretation?” by Butterworth et al.
Authors: Rochet Marie-Joëlle , Rice Jake C. 
Published: February 2010

Abstract
Rochet, M-J., and Rice, J. C. 2010. Comment on “Purported flaws in management strategy evaluation: basic problems or misinterpretation?” by Butterworth et al. – ICES Journal of Marine Science, 67: 575–576. Simulation-based management strategy evaluation is a valuable tool, when appropriately implemented. Implementation, however, may not always have been appropriate, and some reasons are provided why perhaps there is incomplete faith in certain of its technical aspects, such as knowing the distribution of the parameters of population processes from the information in limited datasets. A management strategy that has been evaluated by simulation should not be used as an “autopilot”, because even the most competent of experts can develop autopilots with imperfect and incomplete knowledge of reality, and all information should be incorporated when decisions have to be made.
PEPR2 Is a Second Receptor for the Pep1 and Pep2 Peptides and Contributes to Defense Responses inArabidopsis
Authors: Yamaguchi Yube , Huffaker Alisa , Bryan Anthony C. , Tax Frans E. , Ryan Clarence A. 
Published: February 2010

AbstractPep1 is a 23–amino acid peptide that enhances resistance to a root pathogen, Pythium irregulare. Pep1 and its homologs (Pep2 to Pep7) are endogenous amplifiers of innate immunity of Arabidopsis thaliana that induce the transcription of defense-related genes and bind to PEPR1, a plasma membrane leucine-rich repeat (LRR) receptor kinase. Here, we identify a plasma membrane LRR receptor kinase, designated PEPR2, that has 76% amino acid similarity to PEPR1, and we characterize its role in the perception of Pep peptides and defense responses. Both PEPR1 and PEPR2 were transcriptionally induced by wounding, treatment with methyl jasmonate, Pep peptides, and pathogen-associated molecular patterns. The effects of Pep1 application on defense-related gene induction and enhancement of resistance to Pseudomonas syringae pv tomato DC3000 were partially reduced in single mutants of PEPR1 and PEPR2 and abolished completely in double mutants. Photoaffinity labeling and binding assays using transgenic tobacco (Nicotiana tabacum) cells expressing PEPR1 and PEPR2 clearly demonstrated that PEPR1 is a receptor for Pep1-6 and that PEPR2 is a receptor for Pep1 and Pep2. Our analysis demonstrates differential binding affinities of two receptors with a family of peptide ligands and the corresponding physiological effects of the specific receptor–ligand interactions. Therefore, we demonstrate that, through perception of Peps, PEPR1 and PEPR2 contribute to defense responses in Arabidopsis.
Design and reliability prediction of a distributed landing gear control system
Authors: Lu Lixuan , Lei Jianhe 
Published: February 2010

PurposeProper function of landing gear plays a crucial role in the safe operation of an airplane. Traditional landing gear control system utilizes centralized control technology. The relatively heavy wire harness and low reliability accompanied with this technology make it logical to transfer from traditional control to real‐time distributed control. This paper aims to look into a new landing gear control system based on time‐triggered architecture (TTA).Design/methodology/approachIn this paper, a new landing gear control system based on TTA is proposed. The reliability of the proposed system is investigated using a combination of Markov analysis and MIL‐HDBK‐217 methods.FindingsThe results show that by integration of TTP/C and TTP/A technologies, the advantages of both are achieved. A very high level of reliability is obtained. This increases the confidence when adopting distributed landing gear control technology.Originality/valueThe paper presents a new landing gear control system based on TTA, the reliability of which is very high.
Strategic knowledge management in aerospace industries: a case study
Authors: Jafari Mostafa , Rezaeenour Jalal , Akhavan Peyman , Fesharaki Mehdi N. 
Published: February 2010

PurposeThe objective of this paper is to develop a model for planning and establishment of knowledge management (KM) strategy in one of the Iranian Sub‐stream Aerospace Industries Organization to improve company's performance.Design/methodology/approachThis research tries to use multi‐method approach by integrating balanced score card, which is a renowned strategic management approach, and Nonaka and colleagues' knowledge creation process (socialization, externalization, combination, and internalization model), which is a well‐known knowledge creation and conversion model, being adopted as the foundations of strategic knowledge management model (SKMM).FindingsThe analytical approach identifies eight issues as critical success factors of the knowledge strategy map in this case study. The overall results from the case study are positive as well, thus reflecting the appropriateness of the suggested SKMM model.Research limitations/implicationsSKMM can be used to help forward the plan, establishment and evaluation of KM strategies and initiatives. This helps to ensure that the essential issues are covered during design and implementation phases of KM strategies.Originality/valueThis paper further provides an integrated perspective of KM metrics in high‐tech industries including the aerospace industry. It gives valuable information and guidelines that hopefully will help leaders to consider important issues during performance measurement of KM strategies in organizations.
On library fines
Authors: McMenemy David 
Published: February 2010

PurposeThe purpose of this paper is to discuss the debates around the topic of library fines and consider the arguments highlighted for and against.Design/methodology/approachThe paper provides a reflective overview based on a discussion of the points raised both supporting and rejecting the use of library fines.FindingsIt is argued that fines are a necessary aspect of efficient library operations and to ensure collective responsibility for the collections among members. However the paper queries the reliance of some libraries on the income generated by fines, and questions whether this reliance is in opposition to the role of the library in encouraging efficient use of the stock.Practical implicationsThe paper considers the positives and negatives of a fines culture, and may be useful background for those pondering the topic.Originality/valueThe paper discusses a topic that is of current professional debate as to its efficacy and should of value for those interested in the arguments for and against fines in libraries, and their impact on library usage.
The electronic book: a transformational library technology?
Authors: Joint Nicholas 
Published: February 2010

PurposeThe purpose of this paper is to form one of a series which will give an overview of so‐called “transformational” areas of digital library technology. The aim will be to assess how much real transformation these applications are bringing about, in terms of creating genuine user benefit and also changing everyday library practice.Design/methodology/approachAn overview of the present state of development of the electronic book (e‐book), looking at perceptions in the popular press, statistical data from reputable sources, recent findings from the publicly funded quango Joint Information Systems Committee (JISC), consultants funded by JISC, individual comment from well‐informed writers and observations from contemporary library practice.FindingsThe paper finds that the e‐book has not proven itself as a transformational technology in the context of library services, nor as a consumer product to be sold directly to end users. It does have the potential to be so, if certain problems related to usability, business models and library finding tools are addressed.Research limitations/implicationsThis paper does not engage in a research level investigation of the subject, but does acknowledge and support JISC's recommendations for future research, while putting these into the context of everyday library practice.Practical implicationsThis paper outlines some of the practical challenges faced by librarians in the implementation of e‐book services. These are not always sufficiently acknowledged by publicly funded research that takes place away from the arena of everyday practice.Originality/valueThe approach in this investigation is to present the broader possibilities of e‐book services in a way that is both familiar to library practitioners, and which favourably contrasts the insights and perspectives of the working library profession with those of the higher profile popular press or generously funded research community.
Exploring the use of social software by master of library and information science students
Authors: Al‐Daihani Sultan 
Published: February 2010

PurposeThe purpose of this paper is to explore the perceptions of master of library and information science (MLIS) students of social software.Design/methodology/approachA web‐based questionnaire is used as a survey instrument. The MLIS students at Kuwait University (KU) and the University of Wisconsin‐Milwaukee (UWM) are identified as the population of this study. In total, 132 MLIS students participate in the survey.FindingsThe majority of students from the two schools are aware of social software applications and their use. Blogs, video sharing, collaborative authoring, communication and social networking received the highest mean scores. Their perceptions about online activities, their use of social software and the obstacles to its use were not significantly affected by institutional affiliation. It was further found that the institutional affiliation exhibited significant differences for their perceptions of social software applications in education.Research limitations/implicationsThe sample issues present one of the main limitations of this study and the bias of the survey method.Practical implicationsThe findings of the study can meaningfully contribute to a better understanding of the affect of social software on MLIS students. It also can be applied to the implementation of these applications in library and information science (LIS) education.Originality/valueMost research on social software concentrates on students from other fields; very little research has considered student in LIS. This research is also the first survey to investigate how MLIS students in Kuwait using social software.
Variations in phenolics and antioxidants in Indian onions(Allium cepaL.)
Authors: Dalamu  , Kaur Charanjit , Singh Meenakshi , Walia Shweta , Joshi Subodh , Munshi A.D. 
Published: February 2010

PurposeThe purpose of this paper is to provide a comprehensive evaluation of 34 onion genotypes for their antioxidant activity (AOX) content of phenolics, quercetin and pungency to enable selection of the best genotype for later experiments of variety breeding or to be used as a vector in the improvement of well‐established traditional genotype.Design/methodology/approachA comprehensive screening of 34 onion (red, pink and white) genotypes is carried out in order to determine the variation in phenolics, quercetin and total AOX as potential for breeding for their enhanced levels.FindingsThe AOX in red genotype with highest levels of phenolics is roughly three times higher than commercial white genotype. Pungency levels range from 3.12 to 10.48  μmoles pyruvic acid/g. Mean phenolic and quercetin content ranges from 60.1 to 1094.8 mg gallic acid equivalents/kg and 22.0 to 890.5 mg/kg quercetin, respectively. AOX in red genotype (expressed as μmoles trolox/g) ranges from 1.97 to 5.45 and 3.60 to 6.61 in ferric reducing antioxidant power and cupric ion reducing capacity assays, respectively. Selections, Sel‐383, Sel‐397, Sel‐61‐383, and Inbreds, I‐40, I‐80 and Burgundy are potential genotype with high pungency and AOX.Research limitations/implicationsAn improvement in breeding effort designed to increase the phenolics, quercetin and total AOX in onions (Allium cepaL.) provides selected material for analysis. Onion genotype and breeding lines with improved AOX are identified that would help breeders produce onions high in health promoting compounds.Originality/valueThe paper attempts to examine onion genotypes using standardizedin‐vitroAOX assays.
A systematic review of the quality, content, and context of breakfast consumption
Authors: Mullan Barbara Ann , Singh Monika 
Published: February 2010

PurposeConsumption of breakfast is often associated with important health‐related behaviours. For example, skipping breakfast is related to obesity and eating breakfast is also correlated to cognitive, behavioural, and affective components. The purpose of this paper is to review the breakfast eating literature, and investigate the circumstances under which people consume breakfast, what is actually being consumed, and how much breakfast is eaten therefore.Design/methodology/approachThis systematic review summarises the results from 24 studies which focus on who is eating what, where, and with whom.FindingsAll 24 of the included studies are of a self‐report nature, from which nine were analysed from second‐hand survey data. Sample sizes vary from 100 to a total of 35,119 with a reported participants' age range from two years old to 70 years of age. Ready‐to‐eat cereal and dairy foods are the most commonly consumed breakfast items across the studies. Between 1.7 and 30 per cent of participants are found to skip breakfast and approximately one‐quarter of the studies report that those with lower socio‐economic status, non‐whites, and females were the groups more likely to omit breakfast.Research limitations/implicationsThe evidence provided in this review suggests that there is still considerable variation in studies into breakfast consumption. This has implications for future research into breakfast eating if interventions are based on these studies.Originality/valueThere are very few systematic reviews detailing the quality, context, and content of breakfast consumption and the lack of consistency in the results show the need for further research to be conducted to find a degree of consistency in how breakfast should be defined and measured.
Friction characteristics of brake pads with aramid fiber and acrylic fiber
Authors: Hwan Park Jung , Oh Chung Jin , Rae Kim Hyang 
Published: February 2010

PurposeThe purpose of this paper is to investigate the friction coefficients of aramid and acrylic fibers on brake pads.Design/methodology/approachFiber components used in the present pads are aramid and acrylic fibers, respectively, while keeping other components, such as binders, lubricants, abrasives, fillers the same. Disk FC25 and disk FC17 are used for rotor rubbing test to investigate the friction coefficients with brake pads. The pads are tested by 1/5 scale brake dynamometer, and test mode is modified JASO C406‐P1. The results are analyzed with the friction coefficient and the temperature, transfer film, roughness, and photomicrograph of worn surface on rotors.FindingsThe friction coefficient was mainly determined by the pad material rather than the rotor material, and pads made of aramid fiber had high‐friction coefficient, while pads made of acrylic fiber had low‐friction coefficient, especially under high temperature. Temperature change during braking process was directly related to the initial speed only, and was indifferent to materials or decelerations imposed. In the fade test, the reversal of friction coefficients between the aramid fiber and acrylic fiber pads is determined by the amount of remained amount of respective fiber above 520°C.Originality/valueEffect of different fiber components, aramid and acrylic fibers, on friction characteristics of pad is sought. Reversal of friction coefficients is determined by the thermal stability of fibers used for pads.
Building relevance amidst the content revolution
Authors: Bosanquet Lyn 
Published: February 2010

PurposeThere has been much discussion in the past two decades about the need for the library profession to change. The prophets of doom and gloom have spoken loudly about the profession's lack of relevance and the consequence of this irrelevance. Many have taken notice – marketing campaigns have been introduced, technologies put in place, measures established, etc. All these activities have made some improvements to services but the reality is that is tinkering at the edges rather than taking the giant steps that are actually needed. By investigating the profession's past this paper aims to provide some insight in how to rebuild relevance of the profession i the digital environment.Design/methodology/approachThe challenge is to find a way in which the core skills and competencies of the profession can be shown to add value to work regardless of the context in which they are demonstrated. These skills and capabilities revolve around content; how it is created, how it used, stored, managed, accessed and utilised in order to contribute to an ever‐increasing global body of knowledge. The wider environments in which people work often fail to recognise the complexities of this cycle, and the contribution that the information professional makes to keeping accessible, relevant information available from the desk top. Big decisions whether they be company acquisitions, research methodologies or clinical trials cannot be made without appropriate content. Why then are the content managers, the information professionals, under threat? Are there new skills and capabilities required by information professionals to build value in the content industry that continues to revolutionise?FindingsLibraries need to implement a structure that will allow them to sell, deliver and communicate value. It is time to position the profession as a central player in the digitised information landscape.Originality/valueThe paper provides a high level view articulating what needs to be done for the Information Professional to take their place in the brave new information rich world.
Knowledge management and its potential applicability for libraries
Authors: Sarrafzadeh Maryam , Martin Bill , Hazeri Afsaneh 
Published: February 2010

PurposeThis paper aims to discuss the applications of knowledge management (KM) for library practice.Design/methodology/approachThe paper starts by reviewing the relevant literature and then the results of an empirical study which investigated the perceptions of LIS community on the relevance of KM to libraries. The involvement of libraries in KM programs is also presented.FindingsThe results show that the LIS community exhibits a positive attitude towards introducing KM to libraries, and not only because this could bring libraries closer to their parent organization, but also because it might help them to survive in an increasingly challenging environment.Practical implicationsAlthough there are some indicators of involvement of libraries in KM in published case studies (through activities such as development of intranets and institutional repositories of content management and embedding information literacy instruction in the curriculum and employing web 2.0 technologies for knowledge sharing), libraries are still in the early stage of understanding the potential implications of KM.Originality/valueThe paper focuses on KM in the library community.