bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome analysis of the proteorhodopsin-containing marine bacterium
Polaribacter
sp. MED152 (Flavobacteria)
Authors: González José M. , Fernández-Gómez Beatriz , Fernàndez-Guerra Antoni , Gómez-Consarnau Laura , Sánchez Olga , Coll-Lladó Montserrat , del Campo Javier , Escudero Lorena , Rodríguez-Martínez Raquel , Alonso-Sáez Laura , Latasa Mikel , Paulsen Ian , Nedashkovskaya Olga , Lekunberri Itziar , Pinhassi Jarone , Pedrós-Alió Carlos
Published: June 2008

Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However, a comparable analysis of the Bacteroidetes, the third major bacterioplankton group, is still lacking. In the present paper, we report on the genome of
Polaribacter
sp. strain MED152. On the one hand, MED152 contains a substantial number of genes for attachment to surfaces or particles, gliding motility, and polymer degradation. This agrees with the currently assumed life strategy of marine Bacteroidetes. On the other hand, it contains the proteorhodopsin gene, together with a remarkable suite of genes to sense and respond to light, which may provide a survival advantage in the nutrient-poor sun-lit ocean surface when in search of fresh particles to colonize. Furthermore, an increase in CO
2
fixation in the light suggests that the limited central metabolism is complemented by anaplerotic inorganic carbon fixation. This is mediated by a unique combination of membrane transporters and carboxylases. This suggests a dual life strategy that, if confirmed experimentally, would be notably different from what is known of the two other main bacterial groups (the autotrophic cyanobacteria and the heterotrophic proteobacteria) in the surface oceans. The
Polaribacter
genome provides insights into the physiological capabilities of proteorhodopsin-containing bacteria. The genome will serve as a model to study the cellular and molecular processes in bacteria that express proteorhodopsin, their adaptation to the oceanic environment, and their role in carbon-cycling.
Osteoblasts induce Ca
2+
oscillation-independent NFATc1 activation during osteoclastogenesis
Authors: Kuroda Yukiko , Hisatsune Chihiro , Nakamura Takeshi , Matsuo Koichi , Mikoshiba Katsuhiko
Published: June 2008

Intercellular cross-talk between osteoblasts and osteoclasts is important for controlling bone remolding and maintenance. However, the precise molecular mechanism by which osteoblasts regulate osteoclastogenesis is still largely unknown. Here, we show that osteoblasts can induce Ca
2+
oscillation-independent osteoclastogenesis. We found that bone marrow-derived monocyte/macrophage precursor cells (BMMs) lacking inositol 1,4,5-trisphosphate receptor type2 (IP
3
R2) did not exhibit Ca
2+
oscillation or differentiation into multinuclear osteoclasts in response to recombinant receptor activator of NF-κB ligand/macrophage colony-stimulating factor stimulation. IP
3
R2 knockout BMMs, however, underwent osteoclastogenesis when they were cocultured with osteoblasts or
in vivo
in the absence of Ca
2+
oscillation. Furthermore, we found that Ca
2+
oscillation-independent osteoclastogenesis was insensitive to FK506, a calcineurin inhibitor. Taken together, we conclude that both Ca
2+
oscillation/calcineurin-dependent and -independent signaling pathways contribute to NFATc1 activation, leading to efficient osteoclastogenesis
in vivo
.
Ecocultural basis of cognition: Farmers and fishermen are more holistic than herders
Authors: Uskul Ayse K. , Kitayama Shinobu , Nisbett Richard E.
Published: June 2008

It has been proposed that social interdependence fosters holistic cognition, that is, a tendency to attend to the broad perceptual and cognitive field, rather than to a focal object and its properties, and a tendency to reason in terms of relationships and similarities, rather than rules and categories. This hypothesis has been supported mostly by demonstrations showing that East Asians, who are relatively interdependent, reason and perceive in a more holistic fashion than do Westerners. We examined holistic cognitive tendencies in attention, categorization, and reasoning in three types of communities that belong to the same national, geographic, ethnic, and linguistic regions and yet vary in their degree of social interdependence: farming, fishing, and herding communities in Turkey's eastern Black Sea region. As predicted, members of farming and fishing communities, which emphasize harmonious social interdependence, exhibited greater holistic tendencies than members of herding communities, which emphasize individual decision making and foster social independence. Our findings have implications for how ecocultural factors may have lasting consequences on important aspects of cognition.
Counter-hegemonic language practices and ideologies
Authors: Achugar Mariana
Published: June 2008

This article examines how local norms for Spanish use in a multilingual Southwest Texas border setting respond to and contest dominant monolingual ideologies. The analysis focuses on notions of what languages are legitimate for use in the public sphere in this community and on the benefits of engaging in particular communicative practices. The corpus analyzed comes from interviews with key members of the university (president, program director, professor) and from newspaper articles published in the local newspaper. The article shows how institutional actors from the media and education contest dominant monolingual language ideologies by situating these views historically and connecting them to key conceptual metaphors that encapsulate language ideologies. In doing so, these institutional actors challenge national ideologies that construct monolingualism and standard ‘English’ as the natural and only option connected to social and economic success, offering Spanish and bilingualism as legitimate alternatives.
La frontera Uruguay–Brasil
Authors: Caviglia Serrana , Bertolotti Virginia , Coll Magdalena
Published: June 2008

Este artículo analiza el contacto entre el español y el portugués en la frontera Uruguay-Brasil en el siglo XIX a través de documentos judiciales del Archivo General de la Nación, Uruguay. Primeramente establecimos una tipología de los documentos que nos permitió poner de manifiesto la existencia de una fluida comunicación interlíngüística. Por otra parte, al correlacionar esta tipología con el tipo de interferencias encontradas en los textos, pudimos dar cuenta de los distintos tipos de contacto atestiguados en nuestro corpus. Por último, nos preguntamos si los textos del corpus podían ser considerados como manifestaciones tempranas del actual vernacular de frontera. El análisis propuesto nos proporcionó argumentos significativos para descartar tal posibilidad.
Las metarrepresentaciones en el español hablado
Authors: Ruiz Gurillo Leonor
Published: June 2008

Este artículo se ocupa de diversos procedimientos de metarrepresentación en el español hablado: el discurso directo y la ironía. Se establecen diferencias entre diversas habilidades metarrepresentacionales, como el discurso directo, la metáfora o los evidenciales, por un lado, y la ironía, por otro, ya que esta última constituye una habilidad de orden superior que puede emplear aquellas como indicadores. El análisis en metarrepresentaciones aporta una visión más compleja de tales hechos pragmáticos. Asimismo, el examen de ejemplos reales de conversación permite profundizar en casos no prototípicos.
Representaciones dramáticas de una variable lingüística
Authors: Moyna María Irene , Ceballos Beatriz Vanni
Published: June 2008

El presente estudio es un análisis cuantitativo de las representaciones teatrales del tratamiento de segunda persona del singular en el español del Río de la Plata a comienzos del siglo XX. Se basa en dieciocho obras de teatro escritas entre 1886 y 1911, en cada una de las cuales se contabilizaron todos los verbos de segunda persona (tuteantes y voseantes) y se clasificaron según variables sociolingüísticas del hablante y el interlocutor (clase, edad, género). Las obras reflejan una sociedad que en general prefiere el voseo sobre el tuteo, en concordancia con datos provenientes de otras fuentes tales como cartas personales. Sin embargo, las formas no se distribuyen uniformemente en todos los grupos de hablantes. Los hablantes mayores y de clase alta aparecen representados más a menudo como usuarios de tuteo, mientras que la clase baja urbana y los personajes del campo prefieren el voseo. La elección también se correlaciona con diferencias entre el sexo y la edad del hablante y su interlocutor, y actúa por lo tanto como un indicador del grado de cortesía de los intercambios conversacionales. El voseo es más frecuente en intercambios entre personajes del mismo género que de género diferente. Los personajes mayores, especialmente los hombres, reciben más tuteo que los jóvenes. Finalmente, los autores ponen de manifiesto actitudes más favorables hacia el tuteo cuando se lo atribuyen a los protagonistas, independientemente de su identificación social.
Dar + gerund in Ecuadorian Highland Spanish
Authors: Olbertz Hella
Published: June 2008

The benefactive construction dar + gerund is used in the North Andean region only and is unknown elsewhere in the Spanish-speaking world. Based on the analysis of spontaneous data from Ecuadorian Highland Spanish, this paper provides a linguististic description of dar + gerund and of the social and pragmatic conditions of its use. Departing from this description, I explain that the construction originates through contact with Ecuadorian Quechua. It is shown that the geographical restriction of the use of dar + gerund is directly related to the specific characteristics of Ecuadorian Quechua.
Objetos directos (nulos) en la frontera dominico-haitiana
Authors: Ortiz López Luis A. , Guijarro-Fuentes Pedro
Published: June 2008

En este trabajo, investigamos los objetos directos nulos (argumentos y pronombres clíticos) en hablantes bilingües y monolingües en la frontera domínico-haitiana, mediante factores funcionales de la marcación diferencial de objetos (persona gramatical, ±animado, ±definido, ±específico). Las variables lingüísticas que más favorecen los objetos directos de tercera persona son la animacidad (que es inherente del referente mismo) y la especificidad, la cual viene determinada por el contexto lingüístico. Sin embargo, son aquellos referentes [+animados] [+específicos] [+definido] los que obligan la presencia del pronombre, mientras que los referentes [−animado] [−específicos] [−definidos] podrían realizarse con objetos directos nulos. En fin, durante la adquisición del acusativo de tercera persona, los adultos bilingües van desarrollando un sistema bipartito en cuanto a la ausencia o presencia de los pronombres de objeto directo: todos los objetos animados y con referencia anafórica específica son, por lo general, expresados de forma explícita a través de un pronombre clítico (generalmente lo) mientras que los demás podrían ser objetos directos, presentes o nulos.
Building research capacity collaboratively: Can we take ownership of our future?
Authors: Munn Pamela
Published: June 2008

This presidential address argues that there is a pressing need in the UK to build educational research capacity at system level and to do so collaboratively. It advances three main arguments for doing so. These are (i) the increasing concentration of research resources; (ii) the dangers of increasing separation of research and initial teacher education; and (iii) the complexity of the links between research, policy and practice. Drawing on evidence about research quality and on demographic trends of academic staff in education departments, it illustrates one approach to collaborative capacity building in Scotland, the Applied Educational Research Scheme. It concludes by drawing attention to the nascent Strategic Forum for Research in Education as an important forum for monitoring the health of educational research.
Examining the impacts of changing land use on biological integrity in streams using Geographical Information Systems and statistical modeling
Authors: Goddard Megan A. , Post Christopher J. , English William R. , Pike Jeremy W.
Published: June 2008

Land-use activities and land cover of a watershed influence chemical and physical properties of streams which may impact the biota of the aquatic ecosystem. This study was designed to investigate the impacts of the conversion of forests to urbanized land, including construction and development impacts of land use conversion on water quality and biological integrity of streams. Land use and land cover changes, habitat conditions, water quality, and sediment loadings were studied in eleven subwatersheds of the Reedy River Watershed in the South Carolina Piedmont Ecoregion. Physical and chemical datasets and land use data were used as inputs to build a multivariate model using stepwise multiple regression to predict two instream biological dependant metrics, including Biotic Index, Final Bioclassification, and two biotic metrics that measure richness and species composition. Univariate statistical analysis among 25 environmental variables and biological indices indicated that watersheds of stable land use differed significantly from watersheds undergoing conversion of forest to urban land uses. Significant correlations were observed between land use and particle size distribution, land use and in-stream physical parameters, and land use and in-stream chemical variables. Multivariate statistical analysis indicated that the principle environmental factors correlated with biological responses were conductivity, land use, and substrate distribution. Significant correlations between Biotic Index, Final Bioclassification, and compositional measures were found with conductivity, suggesting that conductivity may be a good indicator of land use changes and thus a good predictor of biotic indices in these subwatersheds.
Ensemble non-negative matrix factorization methods for clustering protein–protein interactions
Authors: Greene Derek , Cagney Gerard , Krogan Nevan , Cunningham Pádraig
Published: June 2008

Motivation: When working with large-scale protein interaction data, an important analysis task is the assignment of pairs of proteins to groups that correspond to higher order assemblies. Previously a common approach to this problem has been to apply standard hierarchical clustering methods to identify such a groups. Here we propose a new algorithm for aggregating a diverse collection of matrix factorizations to produce a more informative clustering, which takes the form of a ‘soft’ hierarchy of clusters.

Results: We apply the proposed Ensemble non-negative matrix factorization (NMF) algorithm to a high-quality assembly of binary protein interactions derived from two proteome-wide studies in yeast. Our experimental evaluation demonstrates that the algorithm lends itself to discovering small localized structures in this data, which correspond to known functional groupings of complexes. In addition, we show that the algorithm also supports the assignment of putative functions for previously uncharacterized proteins, for instance the protein YNR024W, which may be an uncharacterized component of the exosome.

Contact:  derek.greene@ucd.ie

Supplementary information:  Supplementary data are available at http://mlg.ucd.ie/nmf.
Modeling immune system control of atherogenesis
Authors: Pappalardo Francesco , Musumeci Salvatore , Motta Santo
Published: June 2008

Motivation: Atherosclerosis is a disease that is present in almost all humans, typically beginning in early adolescence. It is a human disease broadly investigated, that is amenable to quantitative analysis. Oxidized low-density lipoproteins (LDLs) and their autoantibodies are involved in the development of atherosclerosis in animal models, but their role in humans is still not clear. Computer models may represent a virtual environment to perform experiments not possible in human volunteers that can provide a useful instrument for monitoring both the evolution of atherosclerotic lesions and to quantify the efficacy of treatments, including vaccines, oriented to reduce the LDLs and their oxidized fraction.

Results: We report the application of an agent-based model to model both the immune response to atherogenesis and the atheromatous plaque progression in a generic artery wall. The level of oxidized LDLs, the immune humoral response with production of autoantibodies, the macrophages activity and the formation of foam cells are in good agreement with available clinical data, including the formation of atheromatous plaques in patients affected by hypercholesterolemia.

Availability: The model is available at http://www.immunogrid.eu/atherogenesis/

Contact:  francesco@dmi.unict.it
Sample size for positive and negative predictive value in diagnostic research using case–control designs
Authors: Steinberg David M. , Fine Jason , Chappell Rick
Published: June 2008

Important properties of diagnostic methods are their sensitivity, specificity, and positive and negative predictive values (PPV and NPV). These methods are typically assessed via case–control samples, which include one cohort of cases known to have the disease and a second control cohort of disease-free subjects. Such studies give direct estimates of sensitivity and specificity but only indirect estimates of PPV and NPV, which also depend on the disease prevalence in the tested population. The motivating example arises in assay testing, where usage is contemplated in populations with known prevalences. Further instances include biomarker development, where subjects are selected from a population with known prevalence and assessment of PPV and NPV is crucial, and the assessment of diagnostic imaging procedures for rare diseases, where case–control studies may be the only feasible designs. We develop formulas for optimal allocation of the sample between the case and control cohorts and for computing sample size when the goal of the study is to prove that the test procedure exceeds pre-stated bounds for PPV and/or NPV. Surprisingly, the optimal sampling schemes for many purposes are highly unbalanced, even when information is desired on both PPV and NPV.
Anti‐Oxidant and Anti‐Hypercholesterolemic Activities of Wasabia japonica
Authors: Lee Young Sun , Yang Jae Ha , Bae Man Jong , Yoo Wang Keun , Ye Shen , Xue Charlie C. L. , Li Chun Guang
Published: June 2008

The effects of Wasabia japonica (WJ) were investigated in vitro and in vivo for their anti‐oxidant and anti‐hypercholesterolemic activities. It was found that the aqueous extracts of WJ leaves (WJL) had strong scavenging activities towards 1,1‐Diphenyl‐2‐picryhydrazyl (DPPH) and nitric oxide (NO) free radicals in cell free systems. WJL also inhibited NO production and the expressions of inducible NO synthase (iNOS) mRNA and enzyme protein, determined by Griess reactions, RT‐PCR or Western blotting respectively in Lipopolysaccharide (LPS)‐stimulated RAW 264.7 macrophages cells. The anti‐hypercholesterolemic effects of WJ diet were investigated in hypercholesterolemia rats. Sprague‐Dawley rats were divided into four groups and were fed with either normal diet (Group 1), or diet containing 1%(w/w) cholesterol (Groups 2, 3 and 4). After 4 weeks, Group 2 was changed to normal diet, Groups 3 and 4 were changed to the diet containing 5% WJ leaf and or 5% WJ root, respectively. 3 weeks after WJ diets, Serum HDL‐cholesterol levels were significantly increased in WJ diet groups compared with the normal diet hypercholesterolemia rats. In contrast, the serum LDL‐cholesterol levels and liver xanthine oxidase (XO) activity in WJ diet groups were significantly decreased. The results indicate that the WJ extracts have significant anti‐oxidant activities, and the WJ diet exhibited anti‐hypercholesterolemic action in high cholesterol diet rats, which was companied with modulations of cholesterol metabolism and decrease in liver XO activity.
Traditional Arabic and Islamic Medicine, a Re‐Emerging Health Aid
Authors: Azaizeh Hassan , Saad Bashar , Cooper Edwin , Said Omar
Published: June 2008

Complementary medicine is a formal method of health care in most countries of the ancient world. It is expected to become more widely integrated into the modern medical system, including the medical curriculum. Despite the perception of modern medicine as more efficacious, traditional medicine continues to be practiced. More than 70% of the developing world′s population still depends primarily on the complementary and alternative systems of medicine (CAM). In rural areas, cultural beliefs and practices often lead to self‐care, home remedies or consultation with traditional healers. Herbal medicine can be broadly classified into four basic systems as follows: Traditional Chinese Herbalism, Ayurvedic Herbalism, Western Herbalism—which originally came from Greece and Rome to Europe and then spread to North and South America and Traditional Arabic and Islamic Medicine (TAIM). There is no doubt that today the concept of Arabic traditional herbal medicine is a part of modern life in the Middle East, and it is acquiring worldwide respect, with growing interest among traditional herbalists and the scientific community. TAIM therapies have shown remarkable success in healing acute as well as chronic diseases and have been utilized by people in most countries of the Mediterranean who have faith in spiritual healers. TAIM is the first choice for many in dealing with ailments such as infertility, epilepsy, psychosomatic troubles and depression. In parallel, issues of efficacy and safety of complementary medicine have become increasingly important and supervision of the techniques and procedures used is required for commercial as well as traditional uses. More research is therefore needed to understand this type of medicine and ensure its safe usage. The present review will discuss the status of traditional Arab medicine (particularly herbal medicine), including the efficacy and toxicity of specific medicinal preparations, with an emphasis on the modern in vitro and in vivo techniques.
Alfred Chandler and the Importance of Organization
Authors: Jones Geoffrey
Published: June 2008

Alfred D. Chandler entered my professional life incrementally rather than dramatically.As a student of economic history at CambridgeUniversity in Britain in the early 1970s, I barely encountered his name. British universities had their own long traditions in business and economic history, including a strong interest in entrepreneurship and in government policies toward industry. Most British scholars were not especially enthusiastic about ideas from across the Atlantic, whether the methodological approach of the new economic history of Robert Fogel, or Chandler's organizational synthesis. Cambridge was an especially closed academic world, with a strong assumption that little that happened outside its delightful campus could be really important. It was not until 1979, when I was recruited by the Business History Unit at the London School of Economics (LSE), headed by Chandler's (then) acolyte Leslie Hannah, that I read Strategy and Structure, nearly two decades after it was published.
Beyond Chandler?
Authors: Scranton Philip
Published: June 2008

Unlike several of my colleagues whose retrospective essays are included in this special section, I did not have a personal relationship with Alfred DuPont Chandler, though during the 1980s he did invite me to present a discussion of my first book Proprietary Capitalism at his Harvard business history seminar. I also met Dr. Chandler frequently at Business History Conference meetings, where I found him ever-gracious, indifferent to criticism, and supportive of diverse projects whether allied with or tangential to his own. Thus here I offer some reflections on our discipline and its current situation, taking Chandler's publications as a point of departure.
Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping
Authors: Misceo Doriana , Capozzi Oronzo , Roberto Roberta , Dell’Oglio Maria P. , Rocchi Mariano , Stanyon Roscoe , Archidiacono Nicoletta
Published: June 2008

In this study we characterized the extension, reciprocal arrangement, and orientation of syntenic chromosomal segments in the lar gibbon (Hylobates lar, HLA) by hybridization of a panel of ∼1000 human BAC clones. Each lar gibbon rearrangement was defined by a splitting BAC clone or by two overlapping clones flanking the breakpoint. A reconstruction of the synteny arrangement of the last common ancestor of all living lesser apes was made by combining these data with previous results in Nomascus leucogenys, Hoolock hoolock, and Symphalangus syndactylus. The definition of the ancestral synteny organization facilitated tracking the cascade of chromosomal changes from the Hominoidea ancestor to the present day karyotype of Hylobates and Nomascus. Each chromosomal rearrangement could be placed within an approximate phylogenetic and temporal framework. We identified 12 lar-specific rearrangements and five previously undescribed rearrangements that occurred in the Hylobatidae ancestor. The majority of the chromosomal differences between lar gibbons and humans are due to rearrangements that occurred in the Hylobatidae ancestor (38 events), consistent with the hypothesis that the genus Hylobates is the most recently evolved lesser ape genus. The rates of rearrangements in gibbons are 10 to 20 times higher than the mammalian default rate. Segmental duplication may be a driving force in gibbon chromosome evolution, because a consistent number of rearrangements involves pericentromeric regions (10 events) and centromere inactivation (seven events). Both phenomena can be reasonably supposed to have strongly contributed to the euchromatic dispersal of segmental duplications typical of pericentromeric regions. This hypothesis can be more fully tested when the sequence of this gibbon species becomes available. The detailed synteny map provided here will, in turn, substantially facilitate sequence assembly efforts.
Metabolome Analysis of Biosynthetic Mutants Reveals a Diversity of Metabolic Changes and Allows Identification of a Large Number of New Compounds in Arabidopsis
Authors: Böttcher Christoph , von Roepenack-Lahaye Edda , Schmidt Jürgen , Schmotz Constanze , Neumann Steffen , Scheel Dierk , Clemens Stephan
Published: June 2008

Metabolomics is facing a major challenge: the lack of knowledge about metabolites present in a given biological system. Thus, large-scale discovery of metabolites is considered an essential step toward a better understanding of plant metabolism. We show here that the application of a metabolomics approach generating structural information for the analysis of Arabidopsis (Arabidopsis thaliana) mutants allows the efficient cataloging of metabolites. Fifty-six percent of the features that showed significant differences in abundance between seeds of wild-type, transparent testa4, and transparent testa5 plants could be annotated. Seventy-five compounds were structurally characterized, 21 of which could be identified. About 40 compounds had not been known from Arabidopsis before. Also, the high-resolution analysis revealed an unanticipated expansion of metabolic conversions upstream of biosynthetic blocks. Deficiency in chalcone synthase results in the increased seed-specific biosynthesis of a range of phenolic choline esters. Similarly, a lack of chalcone isomerase activity leads to the accumulation of various naringenin chalcone derivatives. Furthermore, our data provide insight into the connection between p-coumaroyl-coenzyme A-dependent pathways. Lack of flavonoid biosynthesis results in elevated synthesis not only of p-coumarate-derived choline esters but also of sinapate-derived metabolites. However, sinapoylcholine is not the only accumulating end product. Instead, we observed specific and sophisticated changes in the complex pattern of sinapate derivatives.
Interactions between theS-Domain Receptor Kinases and AtPUB-ARM E3 Ubiquitin Ligases Suggest a Conserved Signaling Pathway in Arabidopsis
Authors: Samuel Marcus A. , Mudgil Yashwanti , Salt Jennifer N. , Delmas Frédéric , Ramachandran Shaliny , Chilelli Andrea , Goring Daphne R.
Published: June 2008

The Arabidopsis (Arabidopsis thaliana) genome encompasses multiple receptor kinase families with highly variable extracellular domains. Despite their large numbers, the various ligands and the downstream interacting partners for these kinases have been deciphered only for a few members. One such member, the S-receptor kinase, is known to mediate the self-incompatibility (SI) response in Brassica. S-receptor kinase has been shown to interact and phosphorylate a U-box/ARM-repeat-containing E3 ligase, ARC1, which, in turn, acts as a positive regulator of the SI response. In an effort to identify conserved signaling pathways in Arabidopsis, we performed yeast two-hybrid analyses of various S-domain receptor kinase family members with representative Arabidopsis plant U-box/ARM-repeat (AtPUB-ARM) E3 ligases. The kinase domains from S-domain receptor kinases were found to interact with ARM-repeat domains from AtPUB-ARM proteins. These kinase domains, along with M-locus protein kinase, a positive regulator of SI response, were also able to phosphorylate the ARM-repeat domains in in vitro phosphorylation assays. Subcellular localization patterns were investigated using transient expression assays in tobacco (Nicotiana tabacum) BY-2 cells and changes were detected in the presence of interacting kinases. Finally, potential links to the involvement of these interacting modules to the hormone abscisic acid (ABA) were investigated. Interestingly, AtPUB9 displayed redistribution to the plasma membrane of BY-2 cells when either treated with ABA or coexpressed with the active kinase domain of ARK1. As well, T-DNA insertion mutants for ARK1 and AtPUB9 lines were altered in their ABA sensitivity during germination and acted at or upstream of ABI3, indicating potential involvement of these proteins in ABA responses.
Channelrhodopsin-1 Initiates Phototaxis and Photophobic Responses inChlamydomonasby Immediate Light-Induced Depolarization
Authors: Berthold Peter , Tsunoda Satoshi P. , Ernst Oliver P. , Mages Wolfgang , Gradmann Dietrich , Hegemann Peter
Published: June 2008

Channelrhodopsins (CHR1 and CHR2) are light-gated ion channels acting as sensory photoreceptors in Chlamydomonas reinhardtii. In neuroscience, they are used to trigger action potentials by light in neuronal cells, tissues, or living animals. Here, we demonstrate that Chlamydomonas cells with low CHR2 content exhibit photophobic and phototactic responses that strictly depend on the availability of CHR1. Since CHR1 was described as a H+-channel, the ion specificity of CHR1 was reinvestigated in Xenopus laevis oocytes. Our experiments show that, in addition to H+, CHR1 also conducts Na+, K+, and Ca2+. The kinetic selectivity analysis demonstrates that H+ selectivity is not due to specific translocation but due to selective ion binding. Purified recombinant CHR1 consists of two isoforms with different absorption maxima, CHR1505 and CHR1463, that are in pH-dependent equilibrium. Thus, CHR1 is a photochromic and protochromic sensory photoreceptor that functions as a light-activated cation channel mediating phototactic and photophobic responses via depolarizing currents in a wide range of ionic conditions.
Targeted Degradation of the Cyclin-Dependent Kinase Inhibitor ICK4/KRP6 by RING-Type E3 Ligases Is Essential for Mitotic Cell Cycle Progression duringArabidopsisGametogenesis
Authors: Liu Jingjing , Zhang Yiyue , Qin Genji , Tsuge Tomohiko , Sakaguchi Norihiro , Luo Guo , Sun Kangtai , Shi Dongqiao , Aki Shiori , Zheng Nuoyan , Aoyama Takashi , Oka Atsuhiro , Yang Weicai , Umeda Masaaki , Xie Qi , Gu Hongya , Qu Li-Jia
Published: June 2008

Following meiosis, plant gametophytes develop through two or three rounds of mitosis. Although the ontogeny of gametophyte development has been defined in Arabidopsis thaliana, the molecular mechanisms regulating mitotic cell cycle progression are not well understood. Here, we report that RING-H2 group F 1a (RHF1a) and RHF2a, two RING-finger E3 ligases, play an important role in Arabidopsis gametogenesis. The rhf1a rhf2a double mutants are defective in the formation of male and female gametophytes due to interphase arrest of the mitotic cell cycle at the microspore stage of pollen development and at female gametophyte stage 1 of embryo sac development. We demonstrate that RHF1a directly interacts with and targets a cyclin-dependent kinase inhibitor ICK4/KRP6 (for Interactors of Cdc2 Kinase 4/Kip-related protein 6) for proteasome-mediated degradation. Inactivation of the two redundant RHF genes leads to the accumulation of ICK4/KRP6, and reduction of ICK4/KRP6 expression largely rescues the gametophytic defects in rhf1a rhf2a double mutants, indicating that ICK4/KRP6 is a substrate of the RHF E3 ligases. Interestingly, in situ hybridization showed that ICK4/KRP6 was predominantly expressed in sporophytes during meiosis. Our findings indicate that RHF1a/2a-mediated degradation of the meiosis-accumulated ICK4/KRP6 is essential to ensure the progression of subsequent mitoses to form gametophytes in Arabidopsis.
Bemused by bibliometrics: using citation analysis to evaluate research quality
Authors: Joint Nicholas
Published: June 2008

Purpose

The purpose of this paper is to examine the way in which library and information science (LIS) issues have been handled in the formulation of recent UK Higher Education policy concerned with research quality evaluation.

Design/methodology/approach

A chronological review of decision making about digital rights arrangements for the 2008 Research Assessment Exercise (RAE), and of recent announcements about the new shape of metrics‐based assessment in the Research Excellence Framework, which supersedes the RAE. Against this chronological framework, the likely nature of LIS practitioner reactions to the flow of decision making is suggested.

Findings

It was found that a weak grasp of LIS issues by decision makers undermines the process whereby effective research evaluation models are created. LIS professional opinion should be sampled before key decisions are made.

Research limitations/implications

This paper makes no sophisticated comments on the complex research issues underlying advanced bibliometric research evaluation models. It does point out that sophisticated and expensive bibliometric consultancies arrive at many conclusions about metrics‐based research assessment that are common knowledge amongst LIS practitioners.

Practical implications

Practical difficulties arise when one announces a decision to move to a new and specific type of research evaluation indicator before one has worked out anything very specific about that indicator.

Originality/value

In this paper, the importance of information management issues to the mainstream issues of government and public administration is underlined. The most valuable conclusion of this paper is that, because LIS issues are now at the heart of democratic decision making, LIS practitioners and professionals should be given some sort of role in advising on such matters.
Legitimacy for large public libraries in the digital age
Authors: Waller Vivienne
Published: June 2008

Purpose

The purpose of this paper is to critically analyse recent developments in the relationship of large public libraries with digital technologies, suggesting a way of rethinking the future of large public libraries.

Design/methodology/approach

This paper bases its critical analysis on a review of the literature and reference to specific cases. Historical quotes preceding sections augment the argument that many of the current concerns about digital technologies are not new issues for libraries.

Findings

Issues around library take up of digital technology are continuations of debates that have occurred throughout the history of public libraries about the role of the library. In Australia, library policy makers are focusing on technology and an imagined user in an effort to prove the legitimacy of large public libraries to funding bodies, the library profession and library users. Such attempts seem doomed to fail.

Practical implications

Public libraries need to be clear about their purpose as publicly funded institutions in the digital age. This requires a renewed understanding of a library's publics and a critical understanding of the nature of services available using digital technologies.

Originality/value

This paper presents an alternative way of thinking about the future of large public libraries, with much of the discussion also relevant to local public libraries.
An insight into the Matthew effect in Mexico
Authors: Licea de Arenas Judith , Arenas Miguel , Márquez Sergio
Published: June 2008

Purpose

The purpose of this paper is to profile the prizewinners of the most prestigious award in Mexico, the National Prize for Sciences and the Arts and the Emeritus Professorship awarded by the National University of Mexico.

Design/methodology/approach

The paper draws upon data retrieved from the Web of Science (1995‐2006).

Findings

The 68 laureates published 1,175 papers and received a total of 13,443 citations. The most productive scientists were in the age group 65‐69, while those over 75 years of age were the least productive as well as the less cited. Most prizewinners have at least 35 years' experience scientists, who have been active as researchers for 30‐39 years, were the most productive and the most cited.

Research limitations/implications

Results presented in this paper could complement other indicators of research performance used to determine the visibility of Mexican science, research institutions and individuals and whether resources and influence should be distributed more equitably. The operationalization of the Matthew effect could be minimized if awards committees were to correlate bibliometrics with the peer review process in order to reward the most creative researchers.

Originality/value

The paper focuses on research performance of Mexican academics.
Small creative industry firms: a development dilemma?
Authors: Chaston Ian
Published: June 2008

Purpose

The purpose of the paper is to examine whether the standard support service intervention model of providing training programmes to stimulate business growth is an effective economic regeneration model in the case of small creative industry firms.

Design/methodology/approach

A survey of small creative firms was implemented in the south west UK. The aim of the survey was to gain owner/manager views about participation in training.

Findings

The results reveal the majority of firms are interested in a lifestyle based on fulfilling creative aspirations. Very few respondents exhibit any interest in participating in training schemes aimed at enhancing business performance.

Research limitations/implications

The limitations of the research are that it only relates to creative industry firms and was restricted to a single geographic area and only generated data from micro‐enterprises. The implications of these findings are discussed in relation to whether regional development agency policies in rural areas should primarily be directed towards supporting industry‐led expansion of existing creative industry small firm clusters.

Practical implications

The results provide useful guidance in relation to avoiding public sector expenditure on support schemes that are unlikely to stimulate significant economic growth in the small business sector. Additionally a more cost effective approach to stimulating growth in small creative firms outside of metro‐city areas is presented

Originality/value

Previous researchers have raised questions about the benefits of offering business training to small firms. This study provides additional knowledge in relation to this issue. More importantly, however, the study offers conclusions about the possible need for support agencies to radically revise their current strategies in relation to stimulating growth and new job creation in the creative industry sector.
Charisma as a cognitive‐affective phenomenon: a follower‐centric approach
Authors: Jayakody J.A.S.K.
Published: June 2008

Purpose

The intention of this paper is to conceptualize charisma as a multidimensional, cognitive‐affective phenomenon for the reason that the current practice of conceptualization and operationalization of charisma in terms of observable extraordinary behaviour of the leader has diluted “attributed extraordinariness” while disregarding other facets that the theorists assume to be part of charisma.

Design/methodology/approach

The existing literature on charisma in many diverse disciplines is appraised in order to enumerate the dimensions of charisma. Accordingly, the paper presents a working definition of charisma and makes suggestions on developing a scale of charisma as a multidimensional, cognitive‐affective phenomenon.

Findings

The paper concludes that charisma is a cognitive‐affective phenomenon and is characterized by “Leader extraordinariness”, “Leader archetypicality” “Leader group prototypicality” (cognitive dimensions), “Reverence with awe” and “Love with enthusiasm” (affective dimensions).

Research limitations/implications

Other than explaining how a scale of charisma could be developed, the paper also explains how the proposed conceptualization opens up new avenues for the exploration of routinization of charisma and follower psychological dynamics.

Practical implications

While the paper urges leaders to appeal to followers emotionally and to use the impression management techniques, it urges followers to be vigilant about the “dark side of charisma”.

Originality/value

The present paper can be taken as the first attempt at conceptualizing charisma as a multidimensional, cognitive‐affective phenomenon, though charisma has been long thought to be so. As it takes a follower‐centric approach and incorporates many dimensions of charisma which are presently neglected in operationalizing charisma, the suggested scale of charisma will more validly measure the charisma of leaders than scales presently used.
New directions for the biopharma industry in Canada: modelling and empirical findings
Authors: March‐Chorda Isidre , Yagüe‐Perales Rosa M.
Published: June 2008

Purpose

The main purpose of this study is to identify features and trends shaping the business models currently prevailing in the Canadian biopharma industry, by disaggregating the business model analysis into four key areas: value creation, investment strategy, business strategy, success factors

Design/methodology/approach

Results arise from an empirical fieldwork of qualitative nature, undertaken by the end of 2004, involving deep interviews to a broad variety of key stakeholders of the biopharma industry in the Quebec region, including biopharma firms, large pharma firms, venture capital funds, research centers and recognized experts from consultancy firms and Universities.

Findings

Biopharma firms encounter difficulties to bridge the gap between the research innovation focus to the large scale production focus. The biopharma firms need to announce achievable and promising hits in the near future, mainly by filing patents and also through scientific publications, and making believable their prospects to reach the release phase. Venture capitalists and private investors claim for original, innovative and marketable results, keeping away from just imitative enterprises. The one product firms still largely prevail.

Research limitations/implications

Lessons learned through this fieldwork might in the future be complemented with a quantitative survey to biopharma firms in the Quebec region.

Practical implications

When funding biopharma firms, private investors claim for original, innovative and marketable results, keeping away from just imitative enterprises. The business model must evolve, and take into account the quick changes in the environment, coming either from the market or from the technologies and research streams.

Originality/value

Disaggregating the business model analysis into four key areas will make an original contribution to the limited knowledge about expectations and future prospects of the biopharma industry
The “strategy frame” and the four Es of strategy drivers
Authors: Salem Khalifa Azaddin
Published: June 2008

Purpose

There is vast literature and widely different views on strategy. This necessitates an organizing framework that smoothly integrates and places different conceptualizations of strategy in the proper perspective. The purpose of this paper is to clear possible confusion about the concept of strategy and help navigate the different streams of the strategy river with confidence and ease.

Design/methodology/approach

A comprehensive review of strategy literature is undertaken and the underlying principles and governing ideas are extracted. These are reconstructed to form the basis of the “strategy frame”.

Findings

The “strategy frame” produced the four Es of strategy, which represent the strategic thinking drivers behind the different conceptualizations of strategy. The framework attempts to address all major strategy issues and to combine different schools of thought spanning the spectrum of strategy dimensions, tensions, and paradoxes. It interweaves competing schools of thought in the strategy field and conceptualizes them as continuums to illustrate their interplay.

Research limitations/implications

The conceptual nature of the “strategy frame” makes it less useful in answering the questions it helps raise. As such, it is so broad to be used for working out detailed strategies.

Practical implications

The “strategy frame” helps strategists take a bird's eye view to identify critical strategic issues and put them in the proper context of their organization's capacity as it relates to its environment.

Originality/value

The paper attempts to deal with the basic tensions and paradoxes in strategy field in order to develop a hopefully useful framework, which is able to relate them in an integrative way.
A decision‐maker‐centred supplier selection approach for critical supplies
Authors: Micheli Guido J.L
Published: June 2008

Purpose

The purpose of this paper is to investigate the supplier selection issue as a way to mitigate the overall supply risk, through the proposition of a new approach which is as practical as a total cost of ownership approach and, at the same time, a real support for the supplier selection as a decision making issue, rather than an additional constraint for the decision maker.

Design/methodology/approach

A risk efficiency‐based supplier selection (REBaSS) approach is developed for critical supplies, that allows a decision maker to consider the procurement‐related “risk” and “investment” for mitigation/exploitation interventions.

Findings

A present total cost profile (PTCP) related to every supplier to be assessed is portrayed, as a function of the possible investments that can be made to exploit the upside and to mitigate the downside supply risks. A criterion to prioritize interventions is provided, in order to unambiguously portray the PTCP. Guidelines for the PTCP comparison by a decision maker are also proposed.

Research limitations/implications

The wide set of data needed can be a limitation when the available time to perform supplier selection is very short.

Practical implications

The proposed REBaSS approach allows a decision maker to deal with a quantitative and economic evaluation of the potential suppliers. The decisions are not univocal because they depend on the risk proneness of the decision maker.

Originality/value

The paper's view is that REBaSS is the only approach that explicitly takes into account the variability of the output of the supplier evaluation due to the different attitude of every supplier to make a planned mitigation intervention successful.