bluuebunny/crossref_metadata_2025_split huggingface dataset:
CO impedes superfast O
2
binding in
ba
3
cytochrome oxidase from
Thermus thermophilus
Authors: Szundi Istvan , Funatogawa Chie , Fee James A. , Soulimane Tewfik , Einarsdóttir Ólöf 
Published: November 2010

Kinetic studies of heme-copper terminal oxidases using the CO flow-flash method are potentially compromised by the fate of the photodissociated CO. In this time-resolved optical absorption study, we compared the kinetics of dioxygen reduction by
ba
3
cytochrome
c
oxidase from
Thermus thermophilus
in the absence and presence of CO using a photolabile O
2
-carrier. A novel double-laser excitation is introduced in which dioxygen is generated by photolyzing the O
2
-carrier with a 355 nm laser pulse and the fully reduced CO-bound
ba
3
simultaneously with a second 532-nm laser pulse. A kinetic analysis reveals a sequential mechanism in which O
2
binding to heme
a
3
at 90 μM O
2
occurs with lifetimes of 9.3 and 110 μs in the absence and presence of CO, respectively, followed by a faster cleavage of the dioxygen bond (4.8 μs), which generates the
P
intermediate with the concomitant oxidation of heme
b
. The second-order rate constant of 1 × 10
9
M
-1
s
-1
for O
2
binding to
ba
3
in the absence of CO is 10 times greater than observed in the presence of CO as well as for the bovine heart enzyme. The O
2
bond cleavage in
ba
3
of 4.8 μs is also approximately 10 times faster than in the bovine enzyme. These results suggest important structural differences between the accessibility of O
2
to the active site in
ba
3
and the bovine enzyme, and they demonstrate that the photodissociated CO impedes access of dioxygen to the heme
a
3
site in
ba
3
, making the CO flow-flash method inapplicable.
New students' psychological well‐being and its relation to first year academic performance in a UK university
Authors: Topham Phil , Moller Naomi 
Published: November 2010

AbstractAims: This study (1) profiled the well‐being of first year students entering one UK university, and (2) explored whether initial well‐being and year end academic performance were correlated. Method: A total of 117 students (mean age 21, 67% female) completed the Rosenberg Self‐Esteem Scale, Clinical Outcomes in Routine Evaluation‐General Population, and Liebowitz Social Anxiety Scale; academic achievement data were collected from academic records. Results: Almost a quarter of the sample reported quasi‐clinical levels of psychological distress and moderate to very severe social anxiety. Quasi‐clinical levels of psychological distress were associated with low self‐esteem and social anxiety. No statistically significant links were found between well‐being as assessed at the beginning of the first year and academic achievement at the end of the first year. Discussion: The failure to find a link in this study between initial well‐being and academic performance at the end of the first year suggests that further investigation is required to understand how academic achievement is related to student well‐being.
Improving structure alignment-based prediction of SCOP families using Vorolign Kernels
Authors: Hamp Tobias , Birzele Fabian , Buchwald Fabian , Kramer Stefan 
Published: November 2010

Abstract
Motivation: The slow growth of expert-curated databases compared to experimental databases makes it necessary to build upon highly accurate automated processing pipelines to make the most of the data until curation becomes available. We address this problem in the context of protein structures and their classification into structural and functional classes, more specifically, the structural classification of proteins (SCOP). Structural alignment methods like Vorolign already provide good classification results, but effectively work in a 1-Nearest Neighbor mode. Model-based (in contrast to instance-based) approaches so far have been shown to be of limited values due to small classes arising in such classification schemes.
Results: In this article, we describe how kernels defined in terms of Vorolign scores can be used in SVM learning, and explore variants of combined instance-based and model-based learning, up to exclusively model-based learning. Our results suggest that kernels based on Vorolign scores are effective and that model-based learning can yield highly competitive classification results for the prediction of SCOP families.
Availability: The code is made available at: http://wwwkramer.in.tum.de/research/applications/vorolign-kernel.
Contact: kramer@in.tum.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Comparative Functional Genomic Analysis ofSolanumGlandular Trichome Types
Authors: McDowell Eric T. , Kapteyn Jeremy , Schmidt Adam , Li Chao , Kang Jin-Ho , Descour Anne , Shi Feng , Larson Matthew , Schilmiller Anthony , An Lingling , Jones A. Daniel , Pichersky Eran , Soderlund Carol A. , Gang David R. 
Published: November 2010

AbstractGlandular trichomes play important roles in protecting plants from biotic attack by producing defensive compounds. We investigated the metabolic profiles and transcriptomes to characterize the differences between different glandular trichome types in several domesticated and wild Solanum species: Solanum lycopersicum (glandular trichome types 1, 6, and 7), Solanum habrochaites (types 1, 4, and 6), Solanum pennellii (types 4 and 6), Solanum arcanum (type 6), and Solanum pimpinellifolium (type 6). Substantial chemical differences in and between Solanum species and glandular trichome types are likely determined by the regulation of metabolism at several levels. Comparison of S. habrochaites type 1 and 4 glandular trichomes revealed few differences in chemical content or transcript abundance, leading to the conclusion that these two glandular trichome types are the same and differ perhaps only in stalk length. The observation that all of the other species examined here contain either type 1 or 4 trichomes (not both) supports the conclusion that these two trichome types are the same. Most differences in metabolites between type 1 and 4 glands on the one hand and type 6 glands on the other hand are quantitative but not qualitative. Several glandular trichome types express genes associated with photosynthesis and carbon fixation, indicating that some carbon destined for specialized metabolism is likely fixed within the trichome secretory cells. Finally, Solanum type 7 glandular trichomes do not appear to be involved in the biosynthesis and storage of specialized metabolites and thus likely serve another unknown function, perhaps as the site of the synthesis of protease inhibitors.
Spermidine Is a Morphogenetic Determinant for Cell Fate Specification in the Male Gametophyte of the Water FernMarsilea vestita
Authors: Deeb Faten , van der Weele Corine M. , Wolniak Stephen M. 
Published: November 2010

AbstractHere, we show that the polyamine spermidine plays a key role as a morphogenetic determinant during spermatid development in the water fern Marsilea vestita. Spermidine levels rise first in sterile jacket cells and then increase dramatically in spermatogenous cells as the spermatids mature. RNA interference and drug treatments were employed to deplete spermidine in the gametophyte at different stages of gametogenesis. Development in spermidine-depleted gametophytes was arrested before the completion of the last round of cell divisions. In spermidine-depleted spermatogenous cells, chromatin failed to condense properly, basal body positioning was altered, and the microtubule ribbon was in disarray. When cyclohexylamine, a spermidine synthase (SPDS) inhibitor, was added at the start of spermatid differentiation, the spermatid nuclei remained round, centrin failed to localize into basal bodies, thus blocking basal body formation, and the microtubule ribbon was completely abolished. In untreated gametophytes, spermidine made in the jacket cells moves into the spermatids, where it is involved in the unmasking of stored SPDS mRNAs, leading to substantial spermidine synthesis in the spermatids. We found that treating spores directly with spermidine or other polyamines was sufficient to unmask a variety of stored mRNAs in gametophytes and arrest development. Differences in patterns of transcript distribution after these treatments suggest that specific transcripts reside in different locations in the dry spore; these differences may be linked to the timing of unmasking and translation for that mRNA during development.
ABI4 Mediates Abscisic Acid and Cytokinin Inhibition of Lateral Root Formation by Reducing Polar Auxin Transport in Arabidopsis
Authors: Shkolnik-Inbar Doron , Bar-Zvi Dudy 
Published: November 2010

Abstract
Key steps in a plant's development and adaptation to the environment are the initiation and development of lateral roots (LRs). LR development is regulated by auxin, the major plant hormone promoting LR formation, its counteracting hormones cytokinin, and abscisic acid (ABA). Here, we show that mutating ABSCISIC ACID INSENSITIVE4 (ABI4), which encodes an ABA-regulated AP2 domain transcription factor, results in an increased number of LRs. We show that ABI4 is expressed in roots and that its overexpression impairs LR development. Root expression of ABI4 is enhanced by ABA, and cytokinin and is repressed by auxin. Using hormone response promoters, we show that ABI4 also affects auxin and cytokinin profiles in the root. Furthermore, LR development in abi4 mutants is not altered or inhibited by cytokinin or ABA. Expression of the auxin-efflux carrier protein PIN1 is reduced in ABI4 overexpressors, enhanced in abi4 mutants, and is less sensitive to inhibition by cytokinin and ABA in abi4 mutants than in wild-type plants. Transport levels of exogenously applied auxin were elevated in abi4 mutants and reduced in ABI4 overexpressors. We therefore suggest that ABI4 mediates ABA and cytokinin inhibition of LR formation via reduction of polar auxin transport and that the resulting decrease in root auxin leads to a reduction in LR development.
Members of the LATERAL ORGAN BOUNDARIES DOMAIN Transcription Factor Family Are Involved in the Regulation of Secondary Growth inPopulus
Authors: Yordanov Yordan S. , Regan Sharon , Busov Victor 
Published: November 2010

AbstractRegulation of secondary (woody) growth is of substantial economic and environmental interest but is poorly understood. We identified and subsequently characterized an activation-tagged poplar (Populus tremula × Populus alba) mutant with enhanced woody growth and changes in bark texture caused primarily by increased secondary phloem production. Molecular characterization of the mutation through positioning of the tag and retransformation experiments shows that the phenotype is conditioned by activation of an uncharacterized gene that encodes a novel member of the LATERAL ORGAN BOUNDARIES DOMAIN (LBD) family of transcription factors. Homology analysis showed highest similarity to an uncharacterized LBD1 gene from Arabidopsis thaliana, and we consequently named it Populus tremula × Populus alba (Pta) LBD1. Dominant-negative suppression of Pta LBD1 via translational fusion with the repressor SRDX domain caused decreased diameter growth and suppressed and highly irregular phloem development. In wild-type plants, LBD1 was most highly expressed in the phloem and cambial zone. Two key Class I KNOTTED1-like homeobox genes that promote meristem identity in the cambium were downregulated, while an Altered Phloem Development gene that is known to promote phloem differentiation was upregulated in the mutant. A set of four LBD genes, including the LBD1 gene, was predominantly expressed in wood-forming tissues, suggesting a broader regulatory role of these transcription factors during secondary woody growth in poplar.
Using linked data to classify web documents
Authors: Fripp Dominic 
Published: November 2010

PurposeThe purpose of this paper is to find a relationship between traditional faceted classification schemes and semantic web document annotators, particularly in the linked data environment.Design/methodology/approachA consideration of the conceptual ideas behind faceted classification and linked data architecture is made. Analysis of selected web documents is performed using Calais' Semantic Proxy to support the considerations.FindingsTechnical language aside, the principles of both approaches are very similar. Modern classification techniques have the potential to automatically generate metadata to drive more precise information recall by including a semantic layer.Originality/valueLinked data have not been explicitly considered in this context before in the published literature.
Rental arrangements and risk mitigation of crop insurance and marketing
Authors: Paulson Nicholas D. , Schnitkey Gary D. , Sherrick Bruce J. 
Published: November 2010

PurposeThis study seeks to evaluate the impacts of land rental arrangements on crop insurance and grain marketing decisions.Design/methodology/approachThe analysis is conducted in an Illinois corn‐soybean setting in which optimal marketing and crop insurance decisions are estimated for a risk‐averse producer under typical cash rent and share rent agreements using numerical simulation methods.FindingsResults indicate that the availability of crop insurance impacts the intensity of use of put options under both cash and share rent arrangements. Similar to previous work in this area, revenue insurance is found to cause a substitution away from marketing using put options, while yield insurance is complementary to price risk management alternatives. However, while insurance and marketing play a role under both types of land tenure arrangements, shifting from a cash rent to a share rent agreement provides a relatively greater degree of risk reduction.Practical implicationsThe results suggest that additional research is needed to explain trends in land rental contracts. Crop insurance and other federal programs may provide incentives to switch from share leases to cash rent arrangements. Changes to the design of these programs could facilitate risk management for producers more efficiently.Originality/valueThe unique contribution of this study is the comparison of insurance and marketing decisions under both cash rent and share rent agreements for crop land.
Turning the tables: a faculty‐centered approach to integrating information literacy
Authors: Miller Ielleen R. 
Published: November 2010

PurposeThe purpose of this paper is to describe and analyze Eastern Washington University's Student Research Skills initiative, a three‐year ongoing project, in which librarians work with faculty members from selected departments, to aid them in articulating and integrating information literacy skills into their curricula.Design/methodology/approachThe library selected two departments in 2007‐2008 and another two departments in 2008‐2009. Librarians met with department faculty members multiple times. Librarians asked the faculty: What library research skills do you want students to demonstrate? At what point during the major will they demonstrate the skill? How will you know whether they have the skill? What should the librarian's role be in this process?FindingsParticipating faculty wrote specific information literacy learning outcomes, and revised at least three courses in order to strengthen students' information literacy skills. All of the faculty who answered the survey (12 out of 15) found value in the project, and said they would recommend this project to other faculty. Based on faculty response, the initiative has successfully increased information literacy instruction across the EWU curriculum. Also, it was found that department faculty value librarians' technological skills.Originality/valueMany institutions do not have a campus‐wide program to incorporate information literacy across the curriculum. This paper provides a detailed strategy for librarians to work with department faculty, in order to accomplish this goal. Here, department faculty write their own information literacy learning outcomes. In addition, the EWU project is successful at least in part because the library pays faculty for their time.
The capitalisation rate of the Government Superannuation Fund
Authors: Lally Martin 
Published: November 2010

PurposeThis paper seeks to compare the capitalisation rate offered by the Government Superannuation Fund (GSF) to retiring GSF members with the alternatives of borrowing and sale of the pension entitlements.Design/methodology/approachThe paper uses standard discounted cash flow techniques.FindingsThe principal conclusions are as follows: first, while up to 50 per cent of a GSF member's pension claims can be effectively sold, the restriction that the buyer must be an individual implies a band of possible sale prices with an upper bound equal to that prevailing if sales were unrestricted (present value). Second, borrowing is increasingly favoured over capitalisation as the retirement age declines, and the critical retirement age below which borrowing dominates capitalisation is 64 for men and 66 for women if the GSF member has a spouse at the retirement date and otherwise about three years less. Third, the present value of the pension benefits is well in excess of both the capitalisation rate offered by the GSF and the capitalisation rate implicit in borrowing, implying sale prices even well below present value that are superior to the better of capitalisation and borrowing.Research limitations/implicationsThe analysis treats the retirement age of a GSF member as exogenously determined. However, the analysis also provides insights into the optimal retirement age and this issue is currently the subject of further research.Originality/valueThe paper should provide guidance to GSF members who are contemplating capitalisation of their entitlements.
Unemployed job seekers' access to interactive service work
Authors: Cullen Anne Marie 
Published: November 2010

PurposeThe purpose of this paper is to consider the impact of the shift to a service‐based economy on the employability of unemployed job seekers, specifically focussing on skill acquisition and utilisation. The article considers the provision of training opportunities for unemployed people who are seeking to re‐enter the workplace, and whether such training is taking into account the skills demanded in interactive service work. The article also considers the views of unemployed people towards interactive service work.Design/methodology/approachThe study employs a qualitative approach drawing on interview and focus group data gathered from policymakers, training providers and unemployed job seekers.FindingsThe data suggests there is little existing training provision for interactive service work for unemployed job seekers and that where it does exist it is not geared towards the skills demands of employers. It is also apparent from the research that unemployed job seekers hold a negative view of employment in the interactive service sector, due to both objective and subjective factors.Research limitations/implicationsThe research is limited to one geographical region and research in other regenerating cities could offer potentially different insights.Practical implicationsThe article enjoins with policy debates which are focussing on skills training to enhance employability, considering the importance of apposite skills training. The article also examines the practical and attitudinal barriers to employment that prevent many unemployed jobseekers from gaining access to service sector employment.Originality/valueThe article offers a valuable contribution to ongoing debates surrounding access to employment in the service sector for unemployed job seekers.
Offshoring of white‐collar jobs in the United States and gendered outcomes
Authors: Kongar Ebru , Price Mark 
Published: November 2010

PurposeSince the mid‐1990s, offshore production has become increasingly important in white‐collar, service sector activities in the US economy. This development coincided with a stagnant gender wage gap in the service sector and a slowdown in the narrowing of the overall US gender wage gap over this period. This paper aims to categorize white‐collar service sector occupations into two groups based on whether an occupation is at risk of being offshored and to assess the relative contribution of these two groupings, through their employment and wages, to the trends in the gender wage gap within the service sector and the US economy between 1995 and 2005.Design/methodology/approachStandard occupational decomposition methods are applied to Current Population Survey and Displaced Workers Survey data.FindingsThe findings show that in occupations at risk of being offshored, low‐wage women's employment declined, leading to an artificial increase in the average wage of the remaining women thereby narrowing the gender wage gap. This improvement in the gender wage gap was offset by the relative growth of high‐wage male employment in at‐risk occupations and the widening of the gender wage gap within not‐at‐risk occupations.Originality/valueThese findings contribute to the growing literature on the causes of the stagnation of the US gender wage gap in the 1990s.
The challenges of open access for Korea's national repositories
Authors: Shin Eun‐Ja 
Published: November 2010

PurposeKorea has been at the forefront of the open access movement since 2003, with four nation‐wide repositories built to date. This study seeks to review their current status and to make proposals for further progress.Design/methodology/approachThe study reviews the current status of the four nation‐wide repositories in Korea and identifies their drawbacks and solutions.FindingsKorea's repositories were all built and are operated by government agencies. Their software is superb in contrast with the small volume of contents accumulated. If those repositories are to be invigorated, coordinated efforts are required to publicise the objectives of the repositories, and to try to have all research outputs contributed to the repositories with the cooperation of the operating agencies and researchers.Originality/valueThe study suggests several strategies for invigorating Korea's nation‐wide repositories. If the strategies are implemented in a calm and orderly way, Korea's nation‐wide repositories are expected to be more successful.
Defining the content domain of intercultural competence for global leaders
Authors: Bird Allan , Mendenhall Mark , Stevens Michael J. , Oddou Gary 
Published: November 2010

PurposeResearch on expatriation and global leadership has been characterized by wide variations in defining what constitutes intercultural competence. Greater progress can be achieved if a comprehensive definition of the intercultural competence domain can be established, particularly with regard to the specific context of global leadership. This paper aims to focus on the issues.Design/methodology/approachThe authors conduct an extensive review of the global leadership and expatriation literatures, integrating and synthesizing prior theoretical and empirical efforts to develop a comprehensive domain definition for intercultural competence in the context of global leadership.FindingsThe domain of intercultural competence in the context of global leadership comprised three dimensions – perception management, relationship management and self management. Each dimension is characterized by facets that further delineate aspects of intercultural competence.Research limitations/implicationsThe domain definition of intercultural competence for global leadership appears to be well supported in prior theoretical and empirical work focusing on expatriation and global leadership; however that work was fragmented in nature. A test of the comprehensive model, i.e. all three dimensions and 17 facets, is called for, as well as the validation of an instrument that measures them.Originality/valueThe paper integrates and synthesizes the extensive body of theoretical and empirical work related to intercultural competence and clearly establishes the content domain, thereby enhancing the efficacy of future theoretical and empirical efforts.