bluuebunny/crossref_metadata_2025 huggingface dataset:
Flavobacterium rakeshii sp. nov., isolated from marine sediment, and emended description of

Flavobacterium beibuense

Fu et al. 2011
Authors: Kaur Ishwinder , Kaur Chandandeep , Khan Fazlurrahman , Mayilraj Shanmugam
Published: January 2012

A Gram-negative, non-motile bacterial strain that formed straight rods and straw yellow colonies, designated FCS-5T, was isolated from a marine sediment from the Arabian Sea. The isolate exhibited most of the phenotypic properties expected for a member of the genus

Flavobacterium

. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C17 : 1ω9c and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c). The only isoprenoid quinone was MK-6. The only polyamine was homospermidine and the major polar lipid was phosphatidylethanolamine. The G+C content of the genomic DNA was 32.4 mol%. According to 16S rRNA gene sequence analysis, strain FCS-5T belonged to the genus

Flavobacterium

and exhibited 99.3 % 16S rRNA gene sequence similarity with

Flavobacterium beibuense

F44-8T and 90.9–94.6 % sequence similarity with other members of the genus

Flavobacterium

. The results of physiological and biochemical tests allowed the discrimination of the isolate from its phylogenetic relatives. Strain FCS-5T is a representative of a novel species of the genus

Flavobacterium

, for which the name Flavobacterium rakeshii sp. nov. is proposed. The type strain is FCS-5T ( = MTCC 10967T = JCM 17928T). An emended description of

F. beibuense

is also proposed.
Acinetobacter indicus sp. nov., isolated from a hexachlorocyclohexane dump site
Authors: Malhotra Jaya , Anand Shailly , Jindal Swati , Rajagopal Raman , Lal Rup
Published: January 2012

The taxonomic position of a Gram-negative, non-motile, oxidase negative and catalase positive strain, A648T, isolated from a hexachlorocyclohexane (HCH) dump site located in Lucknow, India, was ascertained by using a polyphasic approach. A comparative analysis of a partial sequence of the rpoB gene and the 16S rRNA gene sequence revealed that strain A648T belonged to the genus

Acinetobacter

. DNA–DNA relatedness values between strain A648T and other closely related members (16S rRNA gene sequence similarity greater than 97 %), namely

Acinetobacter radioresistens

DSM 6976T,

A. venetianus

ATCC 31012T,

A. baumannii

LMG 1041T,

A. parvus

LMG 21765T

A. junii

LMG 998T and

A. soli

JCM 15062T, were found to be less than 8 %. The major cellular fatty acids of strain A648T were 18 : 1ω9c (19.6 %), summed feature 3 (15.9 %), 16 : 0 (10.6 %) and 12 : 0 (6.4 %). The DNA G+C content was 40.4 mol%. The polar lipid profile of strain A648T indicated the presence of diphosphatidylglycerol, phosphatidylethanolamine, followed by phosphatidylglycerol and phosphatidylcholine. The predominant polyamine of strain A648T was 1,3-diaminopropane and moderate amounts of putrescine, spermidine and spermine were also detected. The respiratory quinone consisted of ubiquinone with nine isoprene units (Q-9). On the basis of DNA–DNA hybridization, phenotypic characteristics and chemotaxonomic and phylogenetic comparisons with other members of the genus

Acinetobacter

, strain A648T is found to be a novel species of the genus

Acinetobacter

, for which the name Acinetobacter indicus sp. nov. is proposed. The type strain is A648T ( = DSM 25388T = CCM 7832T).
‘Candidatus Phytoplasma convolvuli’, a new phytoplasma taxon associated with bindweed yellows in four European countries
Authors: Martini Marta , Marcone Carmine , Mitrović Jelena , Maixner Michael , Delić Duška , Myrta Arben , Ermacora Paolo , Bertaccini Assunta , Duduk Bojan
Published: January 2012

Plants of Convolvulus arvensis exhibiting symptoms of undersized leaves, shoot proliferation and yellowing, collectively defined as bindweed yellows, were sampled in different regions of Europe and assessed for phytoplasma infection by PCR amplification using phytoplasma universal rRNA operon primer pairs. Positive results were obtained for all diseased plants. RFLP analysis of amplicons comprising the16S rRNA gene alone or the16S rRNA gene and 16-23S intergenic spacer region indicated that the detected phytoplasmas were distinguishable from all other previously described rRNA gene sequences. Analysis of 16S rRNA gene sequences derived from seven selected phytoplasma strains (BY-S57/11, BY-S62/11, BY-I1015, BY-I1016, BY-BH1, BY-BH2 and BY-G) showed that they were nearly identical (99.9–100 % gene sequence similarity) but shared less than 97.5 % similarity with comparable sequences of other phytoplasmas. Thus, BY phytoplasmas represent a new taxon whose closest relatives are stolbur phytoplasma strains and ‘

Candidatus

Phytoplasma fragariae
’ with which they share 97.2 % and 97.1 % 16S rRNA gene sequence similarity, respectively. Phylogenetic analysis of 16S rRNA gene sequences confirmed that bindweed yellows phytoplasma strains collectively represent a distinct lineage within the phytoplasma clade and share a common ancestor with previously published or proposed ‘Candidatus Phytoplasma’ taxa within a major branch including aster yellows and stolbur phytoplasmas. On the basis of unique 16S rRNA gene sequences and biological properties that include a single host plant species and a geographical distribution limited to parts of Europe, the bindweed yellows (BY) phytoplasmas represent a coherent but discrete taxon, ‘Candidatus Phytoplasma convolvuli’, with strain BY-S57/11 (GenBank accession no. JN833705) as the reference strain.
Toxopsis calypsus gen. nov., sp. nov. (Cyanobacteria, Nostocales) from cave ‘Francthi’, Peloponnese, Greece: a morphological and molecular evaluation
Authors: Lamprinou V. , Skaraki K. , Kotoulas G. , Economou-Amilli A. , Pantazidou A.
Published: January 2012

Representatives of a new cyanobacterial genus, Toxopsis Lamprinou & Pantazidou gen. nov., were found in fresh material from Cave ‘Francthi’ (Peloponnese, Greece) and isolated in cultures. Ecological data relating to the environmental parameters of the sampling sites are provided, such as the photosynthetically active radiation (PAR), temperature and relative humidity. Morphological characteristics and the life cycle of the type species Toxopsis calypsus Lamprinou & Pantazidou sp. nov. were studied using light microscopy and scanning and transmission microscopy. Molecular analysis based on the 16S rRNA gene sequence was also conducted. Toxopsis calypsus sp. nov. is a false-branched nostocalean cyanobacterium with both isopolar and heteropolar filaments bearing mono-pored and bi-pored heterocysts, and also hormogonia and akinetes. Isopolar filaments adhere by the centre to the substrate and are found mainly in fresh material and in young cultures; heteropolar filaments bearing a basic mono-pore heterocyst are dominant in aged (more than one-year-old) cultures. According to the revised taxonomic classification system of Komárek & Anagnostidis (1989) [Komárek, J. & Anagnostidis, K. (1989). Algol Stud, 56, 247–345] based mainly on morphological data, the new genus described here shares morphological characters with both nostocalean families Scytonemataceae and Microchaetaceae, showing similarities in particular to Scytonematopsis contorta [Vaccarino, M. A. & Johansen, J. R. (2011). Fottea 11, 149–161], Microchaetaceae. Molecular data from the 16S rRNA sequence determined in this paper showed that Toxopsis calypsus sp. nov. is more related to the family Microchaetaceae, and the five phylotypes analysed by PCR showed that the closest nostocalean relatives are Tolypothrix distorta SAG 93.79 (GenBank accession no. GQ287651) and Coleodesmium sp. ANT.L52B.5 (AY493596) with 95–96 % and 96 % similarity, respectively. In contrast, the five phylotypes showed a distant similarity to Scytonematopsis contorta (<91 %). The phenotypic and genetic traits strongly supported the classification of the five phylotypes as a new taxon for which the name Toxopsis calypsus Lamprinou & Pantazidou gen. nov., sp. nov. is proposed.
Halomonas ramblicola sp. nov., a moderately halophilic bacterium from Rambla Salada, a Mediterranean hypersaline rambla
Authors: Luque Rocío , Béjar Victoria , Quesada Emilia , Martínez-Checa Fernando , Llamas Inmaculada
Published: January 2012

A moderately halophilic bacterium (strain RS-16T) was isolated from saline soil in Rambla Salada, a Mediterranean hypersaline rambla in Murcia, south-east Spain. Cells of strain RS-16T were Gram-negative rods, oxidase-negative and motile by peritrichous flagella. Strain RS-16T required NaCl for growth, and grew between 1 % and 30 % (w/v) NaCl (optimum, 5–7.5 %), at temperatures of between 4 °C and 41 °C (optimum, 32–37 °C), and at pH values of between 5 and 10 (optimum, pH 7). Strain RS-16T was chemo-organotrophic and its metabolism was respiratory with oxygen and nitrate as terminal electron acceptors. It produced acids from d-glucose and myo-inositol, accumulated poly-β-hydroxyalkanoate granules and produced cream colonies on MY 7.5 % (w/v). The DNA G+C content of strain RS-16T was 56.2 mol%. A comparison of 16S rRNA gene sequences confirmed the relationship of strain RS-16T to species of the genus

Halomonas

. The most phylogenetically related species was

Halomonas cerina

SP4T (97.4 %16S rRNA gene sequence similarity). In DNA–DNA hybridization assays strain RS-16T showed DNA–DNA relatedness values of 62.7±3.09 %, 64.5±1.97 % and 64.7±1.74 % to

Halomonas cerina

CECT 7282T,

Halomonas cerina

CECT 7284 and

Halomonas cerina

CECT 7283, respectively. The major fatty acids of strain RS-16T were C18 : 1ω7c and C16 : 0, and the predominant respiratory lipoquinone was ubiquinone, with nine isoprene units (Q-9). On the basis of these data, strain RS-16T is considered to represent a novel species of the genus

Halomonas

, for which the name Halomonas ramblicola sp. nov. is proposed. The type strain is RS-16T ( = CECT 7896T = LMG 26647T).
The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo
Authors: Satija Rahul , Bradley Robert K.
Published: January 2012

Highly overlapping patterns of genome-wide binding of many distinct transcription factors have been observed in worms, insects, and mammals, but the origins and consequences of this overlapping binding remain unclear. While analyzing chromatin immunoprecipitation data sets from 21 sequence-specific transcription factors active in the Drosophila embryo, we found that binding of all factors exhibits a dose-dependent relationship with “TAGteam” sequence motifs bound by the zinc finger protein Vielfaltig, also known as Zelda, a recently discovered activator of the zygotic genome. TAGteam motifs are present and well conserved in highly bound regions, and are associated with transcription factor binding even in the absence of canonical recognition motifs for these factors. Furthermore, levels of binding in promoters and enhancers of zygotically transcribed genes are correlated with RNA polymerase II occupancy and gene expression levels. Our results suggest that Vielfaltig acts as a master regulator of early development by facilitating the genome-wide establishment of overlapping patterns of binding of diverse transcription factors that drive global gene expression.
Transcriptional Regulation of ArabidopsisMIR168aandARGONAUTE1Homeostasis in Abscisic Acid and Abiotic Stress Responses
Authors: Li Wei , Cui Xiao , Meng Zhaolu , Huang Xiahe , Xie Qi , Wu Heng , Jin Hailing , Zhang Dabing , Liang Wanqi
Published: January 2012

The accumulation of a number of small RNAs in plants is affected by abscisic acid (ABA) and abiotic stresses, but the underlying mechanisms are poorly understood. The miR168-mediated feedback regulatory loop regulates ARGONAUTE1 (AGO1) homeostasis, which is crucial for gene expression modulation and plant development. Here, we reveal a transcriptional regulatory mechanism by which MIR168 controls AGO1 homeostasis during ABA treatment and abiotic stress responses in Arabidopsis (Arabidopsis thaliana). Plants overexpressing MIR168a and the AGO1 loss-of-function mutant ago1-27 display ABA hypersensitivity and drought tolerance, while the mir168a-2 mutant shows ABA hyposensitivity and drought hypersensitivity. Both the precursor and mature miR168 were induced under ABA and several abiotic stress treatments, but no obvious decrease for the target of miR168, AGO1, was shown under the same conditions. However, promoter activity analysis indicated that AGO1 transcription activity was increased under ABA and drought treatments, suggesting that transcriptional elevation of MIR168a is required for maintaining a stable AGO1 transcript level during the stress response. Furthermore, we showed both in vitro and in vivo that the transcription of MIR168a is directly regulated by four abscisic acid-responsive element (ABRE) binding factors, which bind to the ABRE cis-element within the MIR168a promoter. This ABRE motif is also found in the promoter of MIR168a homologs in diverse plant species. Our findings suggest that transcriptional regulation of miR168 and posttranscriptional control of AGO1 homeostasis may play an important and conserved role in stress response and signal transduction in plants.
Trehalose 6-Phosphate Is Required for the Onset of Leaf Senescence Associated with High Carbon Availability
Authors: Wingler Astrid , Delatte Thierry L. , O’Hara Liam E. , Primavesi Lucia F. , Jhurreea Deveraj , Paul Matthew J. , Schluepmann Henriette
Published: January 2012

Trehalose 6-phosphate (T6P) is an important regulator of plant metabolism and development. T6P content increases when carbon availability is high, and in young growing tissue, T6P inhibits the activity of Snf1-related protein kinase (SnRK1). Here, strong accumulation of T6P was found in senescing leaves of Arabidopsis (Arabidopsis thaliana), in parallel with a rise in sugar contents. To determine the role of T6P in senescence, T6P content was altered by expressing the bacterial T6P synthase gene, otsA (to increase T6P), or the T6P phosphatase gene, otsB (to decrease T6P). In otsB-expressing plants, T6P accumulated less strongly during senescence than in wild-type plants, while otsA-expressing plants contained more T6P throughout. Mature otsB-expressing plants showed a similar phenotype as described for plants overexpressing the SnRK1 gene, KIN10, including reduced anthocyanin accumulation and delayed senescence. This was confirmed by quantitative reverse transcription-polymerase chain reaction analysis of senescence-associated genes and genes involved in anthocyanin synthesis. To analyze if the senescence phenotype was due to decreased sugar sensitivity, the response to sugars was determined. In combination with low nitrogen supply, metabolizable sugars (glucose, fructose, or sucrose) induced senescence in wild-type and otsA-expressing plants but to a smaller extent in otsB-expressing plants. The sugar analog 3-O-methyl glucose, on the other hand, did not induce senescence in any of the lines. Transfer of plants to and from glucose-containing medium suggested that glucose determines senescence during late development but that the effects of T6P on senescence are established by the sugar response of young plants.
A Comprehensive Dataset of Genes with a Loss-of-Function Mutant Phenotype in Arabidopsis
Authors: Lloyd Johnny , Meinke David
Published: January 2012

Despite the widespread use of Arabidopsis (Arabidopsis thaliana) as a model plant, a curated dataset of Arabidopsis genes with mutant phenotypes remains to be established. A preliminary list published nine years ago in Plant Physiology is outdated, and genome-wide phenotype information remains difficult to obtain. We describe here a comprehensive dataset of 2,400 genes with a loss-of-function mutant phenotype in Arabidopsis. Phenotype descriptions were gathered primarily from manual curation of the scientific literature. Genes were placed into prioritized groups (essential, morphological, cellular-biochemical, and conditional) based on the documented phenotypes of putative knockout alleles. Phenotype classes (e.g. vegetative, reproductive, and timing, for the morphological group) and subsets (e.g. flowering time, senescence, circadian rhythms, and miscellaneous, for the timing class) were also established. Gene identities were classified as confirmed (through molecular complementation or multiple alleles) or not confirmed. Relationships between mutant phenotype and protein function, genetic redundancy, protein connectivity, and subcellular protein localization were explored. A complementary dataset of 401 genes that exhibit a mutant phenotype only when disrupted in combination with a putative paralog was also compiled. The importance of these genes in confirming functional redundancy and enhancing the value of single gene datasets is discussed. With further input and curation from the Arabidopsis community, these datasets should help to address a variety of important biological questions, provide a foundation for exploring the relationship between genotype and phenotype in angiosperms, enhance the utility of Arabidopsis as a reference plant, and facilitate comparative studies with model genetic organisms.
Suppression of Arabidopsis ARGONAUTE1-Mediated Slicing, Transgene-Induced RNA Silencing, and DNA Methylation by Distinct Domains of the Cucumber mosaic virus 2b Protein
Authors: Duan Cheng-Guo , Fang Yuan-Yuan , Zhou Bang-Jun , Zhao Jian-Hua , Hou Wei-Na , Zhu Hui , Ding Shou-Wei , Guo Hui-Shan
Published: January 2012

Unique among the known plant and animal viral suppressors of RNA silencing, the 2b protein interacts directly with both small interfering RNA (siRNA) and ARGONAUTE1 (AGO1) and AGO4 proteins and is targeted to the nucleolus. However, it is largely unknown which regions of the 111-residue 2b protein determine these biochemical properties and how they contribute to its diverse silencing suppressor activities. Here, we identified a functional nucleolar localization signal encoded within the 61–amino acid N-terminal double-stranded RNA (dsRNA) binding domain (dsRBD) that exhibited high affinity for short and long dsRNA. However, physical interaction of 2b with AGOs required an essential 33-residue region C-terminal to the dsRBD and was sufficient to inhibit the in vitro AGO1 Slicer activity independently of its dsRNA binding activities. Furthermore, the direct 2b–AGO interaction was not essential for the 2b suppression of posttranscriptional gene silencing (PTGS) and RNA-directed DNA methylation (RdDM) in vivo. Lastly, we found that the 2b–AGO interactions in vivo also required the nucleolar targeting of 2b and had the potential to redistribute both the 2b and AGO proteins in nucleus. These findings together suggest that 2b may suppress PTGS and RdDM in vivo by binding and sequestering siRNA and the long dsRNA precursor in a process that is facilitated by its interactions with AGOs in the nucleolus.
The Apoplastic Oxidative Burst Peroxidase in Arabidopsis Is a Major Component of Pattern-Triggered Immunity
Authors: Daudi Arsalan , Cheng Zhenyu , O’Brien Jose A. , Mammarella Nicole , Khan Safina , Ausubel Frederick M. , Bolwell G. Paul
Published: January 2012

In plants, reactive oxygen species (ROS) associated with the response to pathogen attack are generated by NADPH oxidases or apoplastic peroxidases. Antisense expression of a heterologous French bean (Phaseolus vulgaris) peroxidase (FBP1) cDNA in Arabidopsis thaliana was previously shown to diminish the expression of two Arabidopsis peroxidases (peroxidase 33 [PRX33] and PRX34), block the oxidative burst in response to a fungal elicitor, and cause enhanced susceptibility to a broad range of fungal and bacterial pathogens. Here we show that mature leaves of T-DNA insertion lines with diminished expression of PRX33 and PRX34 exhibit reduced ROS and callose deposition in response to microbe-associated molecular patterns (MAMPs), including the synthetic peptides Flg22 and Elf26 corresponding to bacterial flagellin and elongation factor Tu, respectively. PRX33 and PRX34 knockdown lines also exhibited diminished activation of Flg22-activated genes after Flg22 treatment. These MAMP-activated genes were also downregulated in unchallenged leaves of the peroxidase knockdown lines, suggesting that a low level of apoplastic ROS production may be required to preprime basal resistance. Finally, the PRX33 knockdown line is more susceptible to Pseudomonas syringae than wild-type plants. In aggregate, these data demonstrate that the peroxidase-dependent oxidative burst plays an important role in Arabidopsis basal resistance mediated by the recognition of MAMPs.
The Rice Pentatricopeptide Repeat Protein RF5 Restores Fertility in Hong-Lian Cytoplasmic Male-Sterile Lines via a Complex with the Glycine-Rich Protein GRP162
Authors: Hu Jun , Wang Kun , Huang Wenchao , Liu Gai , Gao Ya , Wang Jianming , Huang Qi , Ji Yanxiao , Qin Xiaojian , Wan Lei , Zhu Renshan , Li Shaoqing , Yang Daichang , Zhu Yingguo
Published: January 2012

The cytoplasmic male sterility (CMS) phenotype in plants can be reversed by the action of nuclear-encoded fertility restorer (Rf) genes. The molecular mechanism involved in Rf gene–mediated processing of CMS-associated transcripts is unclear, as are the identities of other proteins that may be involved in the CMS–Rf interaction. In this study, we cloned the restorer gene Rf5 for Hong-Lian CMS in rice and studied its fertility restoration mechanism with respect to the processing of the CMS-associated transcript atp6-orfH79. RF5, a pentatricopeptide repeat (PPR) protein, was unable to bind to this CMS-associated transcript; however, a partner protein of RF5 (GRP162, a Gly-rich protein encoding 162 amino acids) was identified to bind to atp6-orfH79. GRP162 was found to physically interact with RF5 and to bind to atp6-orfH79 via an RNA recognition motif. Furthermore, we found that RF5 and GRP162 are both components of a restoration of fertility complex (RFC) that is 400 to 500 kD in size and can cleave CMS-associated transcripts in vitro. Evidence that a PPR protein interacts directly with a Gly-rich protein to form a subunit of the RFC provides a new perspective on the molecular mechanisms underlying fertility restoration.
The need and viability of a mediation index in Latin American scientific production and publication
Authors: Aguado‐López Eduardo , Adolfo Garduño‐Oropeza Gustavo , Rogel‐Salazar Rosario , Fernanda Zúñiga‐Roca María
Published: January 2012

Purpose

The purpose of this paper is to introduce the online information system Redalyc as an intermediary tool that provides Latin American scientific articles with international standards (mostly related to natural sciences and developed countries) as well as with specific areas to host local research.

Design/methodology/approach

Redalyc is based on a semantic intersection model proposed by Russian semiologist Yuri Lotman. This model allows us to visualize the role played by Redalyc as a mediator between opposites, i.e. local science versus global science, and natural sciences versus social sciences. The paper presents some of the projects Redalyc has developed in conjunction with different countries and different scientific communities.

Findings

The paper describes some characteristics that local projects, similar to Redalyc, must have in order to become an intermediary between scientific journal production indexes that link global parameters for scientific communication with local production. The paper finds that efforts should not only be centered on the development of strategies to change certain inertias that distinguish local social scientific production (e.g. dependence on literary resources, lack of recognition of periodical media), but also on the way they could help these disciplines and local media overcome certain barriers, namely: normalization, language and technological handicaps.

Originality/value

The recognition of Latin American scientific production implies a dual process that not only involves local policies (scientific councils), but also requires producing reliable databases to provide scientists and journal editors with global references on how to produce visible scientific literature and pertinent knowledge for their contexts. Redalyc is currently a database that contributes in both ways.
Latin American scholarly journal databases: a look back to the way forward
Authors: Octavio Alonso‐Gamboa José , Russell Jane M.
Published: January 2012

Purpose

Scholarly journals from Latin America have aspired to reach an adequate level of visibility and impact not only locally, but also in the international arena. Editors have not been alone in this endeavour, other actors in the information chain have also played their part. This article aims to examine the databases (indexing and abstracting services, directories, catalogues and electronic journal portals) produced in Latin America between 1970 and 2009.

Design/methodology/approach

The paper begins with an historical review of the relevant regional initiatives and leads up to an assessment of the present day situation by analysing the contribution made by the databases in the identification, register, visibility, access and use of Latin American scholarly journals.

Findings

The creation of Latin American databases has improved communication and knowledge on publications in the region as useful additions to the scant information provided by international sources. The recent adherence to the principles of the Open Access movement has also potentially improved the visibility and access to publications from the region.

Originality/value

This is the first study to analyse the development of Latin American databases over a period of some 40 years.
Organizing open archives via lightweight ontologies to facilitate the use of heterogeneous collections
Authors: Alfredo Sánchez J. , Auxilio Medina María , Starostenko Oleg , Benitez Antonio , López Domínguez Eduardo
Published: January 2012

Purpose

This paper seeks to focus on the problems of integrating information from open, distributed scholarly collections, and on the opportunities these collections represent for research communities in developing countries. The paper aims to introduce OntOAIr, a semi‐automatic method for constructing lightweight ontologies of documents in repositories such as those provided by the Open Archives Initiative (OAI).

Design/methodology/approach

OntOAIr uses simplified document representations, a clustering algorithm, and ontological engineering techniques.

Findings

The paper presents experimental results of the potential positive impact of ontologies and specifically of OntOAIr on the use of collections provided by OAI.

Research limitations/implications

By applying OntOAIr, scholars who frequently spend many hours organizing OAI information spaces will obtain support that will allow them to speed up the entire research cycle and, expectedly, participate more fully in global research communities.

Originality/value

The proposed method allows human and software agents to organize and retrieve groups of documents from multiple collections. Applications of OntOAIr include enhanced document retrieval. In this paper, the authors focus particularly on document retrieval applications.
Web visibility or wasted opportunity? Case studies from Mexican research institutes
Authors: Russell Jane M. , Ainsworth Shirley , Díaz‐Aguilar Janet
Published: January 2012

Purpose

This paper aims to determine to what extent the scientific production and research activities of a group of National Autonomous University of Mexico (UNAM) research institutes in the sciences, social sciences and humanities are visible on the internet with a view to identifying areas where web presence is not optimal so improvements can be made.

Design/methodology/approach

The authors do this by analysing the relevant information on their web sites and by comparing institutional listings of scientific production between 2005 and 2006, with papers reported in the international, multidisciplinary online services of the Web of Science and Scopus, as well as in Clase and Periódica which cover production in Latin American journals.

Findings

Results indicate general poor visibility of research activities and production in the institutional web sites with only limited access to full text articles. Web sites of the institutes in the sciences score better than those in the humanities and social sciences where book publication is an important research output. The official publication lists in the form of annual reports were found not to accurately represent production with additional papers attributed to the different institutions appearing in commercial databases. It is suggested that more effort should be directed towards improving the information content and access to research data on these institutional web sites, possibly through linkage to an UNAM repository.

Originality/value

This is the first study to critically examine the visibility of research on Mexican academic web sites for which a series of indicators related to the different categories of research information which would ideally be found on institutional pages were developed.
World economic crisis impact on organic products consumption: Costa Rica, 2009
Authors: Aguirre Gonzalez Juan Antonio
Published: January 2012

Purpose

The purpose of this paper is to evaluate the impact of the economic crisis in organic consumption in order to better understand how to meet the emerging challenges that the crisis is creating for future consumption and production of organic products in Costa Rica, and to review the material available in the commercial and scientific literature.

Design/methodology/approach

A sample survey of 63 consumers was carried out based on an average population of 75 visitors every Saturday, the only day of the week that the market takes place. The analytical procedure was divided in two parts: the descriptive statistic's section base on histograms showing the distribution of the variable's responses; and the inferential statistic's analysis which used standardized forward elimination regression modeling to arrive at the final models to explain the importance of the selected variables in each equation, along with a thorough search of the available and the most recent material.

Findings

The profile of the organic consumer in 2009 was very similar to that of 2000, 2004 and 2007. The willingness to pay premiums went down from 25 per cent in 2007, to 15 per cent in 2009 and was associated primarily with irregular availability, limited supply, limited variety and the location of the market. Price was an integral part of all three derived models, something that was not the case in past surveys. Even though consumer's income is very high, the crisis was affecting the purchase of organic products. The hypotheses that the crisis had not affected consumption and willingness to pay were both rejected based on the results obtained.

Research limitations/implications

The crisis is still with us, most of the material available for comparison at this time comes from “commercial surveys”, sources with basically no “hard” research with which to compare the results that were secured in this survey.

Practical implications

The findings can help developing countries in Latin America with similar conditions meet the challenges of the future, as the developing countries overcome the crisis in terms of better policies and strategies.

Originality/value

To the author's knowledge, this is the first paper of its kind in a developing country. It provides evidence of the impact of the economic crisis on organic consumption in a developing country and the author knows of no other in Latin America.
Food safety concern
Authors: Yeung Ruth , Yee Wallace M.S.
Published: January 2012

Purpose

The purpose of this paper is to examine how the incorporation of marketing elements into consumer risk coping strategies affects consumer purchase decision during periods of food safety concern.

Design/methodology/approach

This research used a structured questionnaire administered to a convenience sample of 216 respondents. By using logistic regression, a consumer risk coping framework incorporating marketing strategies was successfully developed to test the impact of brand and quality assurance, price reduction, availability in all stores and endorsement from an independent organization, which may not act alone but combine with each other during food purchase.

Findings

The research confirms that consumers adopt risk coping strategies in time of food risk concern and their coping strategies include marketing elements such as brand and quality assurance, price reduction, availability in all stores and endorsement from an independent organization.

Practical implications

The framework helps marketers to predict the effect of their marketing plan by incorporating consumers' risk coping strategies, in turn to improve consumers' purchase intention when perceived food safety risk exists.

Originality/value

This research demonstrates how marketers can incorporate marketing strategies in a consumer risk coping framework, in order to provide an insight for the industry to evaluate the effectiveness of their marketing strategies in times of food safety concern.
Ethical evaluation by consumers: the role of product harm and disclosure
Authors: Sun Pi‐Chuan , Chen Hsu‐Ping , Wang Kuang‐cheng
Published: January 2012

Purpose

The purpose of this paper is to explore the impacts of product harm, consumers' product knowledge and firms' negative information disclosure on ethical evaluation of a firm, especially, the moderating effects of product knowledge and negative information disclosure.

Design/methodology/approach

A 3×2×2 between‐subject design with three levels of product harm, two levels of product knowledge, and two treatments of negative information was used in this study. The experimental product is diet food.

Findings

The findings reveal that the level of product harm affects consumers' ethical evaluation. Furthermore, the individual's ethical evaluation will influence his or her purchase intention. The main effect of subjective knowledge is significant while its moderating effect is not significant. It is also found that the negative information disclosure will lower consumer's ethical evaluation of a firm, and the effect of product harm on ethical evaluation will be stronger for harmful products than for harmless products when the negative information is disclosed.

Practical implications

Marketers might need to be especially responsive if their practices result in a diminished reputation for their firms and lost sales. Exploiting the vulnerability of consumers or worsening their situation by marketing harmful products might be evaluated as unethical under principles of justice. It is suggested that marketers include increased disclosures of actual product harm levels relative to industry norms.

Originality/value

Consumers' product knowledge and firms' negative information disclosure are integrated into the model, exploring the effect of product harm on consumer's ethical evaluation of a firm and their moderating effects are discussed.
Segmentation of Taiwanese consumers based on trust in the food supply system
Authors: Chen Mei‐Fang
Published: January 2012

Purpose

The purpose of this paper is to segment Taiwanese consumers based on their trust in the food supply system and to demographically characterize each segment so as to aid the actors and institutions involved in the food supply system in formulating more effective communication strategies for different segments and to assist the consumers in increasing their trust in food safety.

Design/methodology/approach

A total of 592 useful responses were elicited as the data input for cluster analysis, repeated measures ANOVA tests, and chi‐square tests.

Findings

Cluster analysis reveals that the 592 respondents in Taiwan can be segmented into three clusters: consumers who are pessimistic, neutral, or optimistic about food safety. Moreover, the repeated measures ANOVA tests for each segment disclose that among the food supply system the foods imported from abroad are perceived by the three clusters to be the least, while the government responsible for food safety inspection and checking the most, trustworthy. The chi‐square test results reveal that the pessimistic consumers seem to be composed of a higher percentage of respondents whose level of education and amount of monthly income are below average.

Practical implications

For food safety a government agency, TFDA, has been set up to be in charge of the task of monitoring conscientiously all of the players in the food supply chain, including the importation system.

Originality/value

This is the first study to segment Taiwanese consumers based on their trust in the food supply system. Based on the findings, suggestions are provided to benefit the actors and institutions involved in the food supply system in Taiwan.
Consumers' perceptions of HPP and PEF food products
Authors: Sonne Anne‐Mette , Grunert Klaus G. , Veflen Olsen Nina , Granli Britt‐Signe , Szabó Erzsébet , Banati Diana
Published: January 2012

Purpose

The purpose of this paper is to examine consumer attitudes towards apple juice produced by means of two new processing technologies, high‐pressure processing (HPP) and pulsed electric field processing (PEF).

Design/methodology/approach

Means‐end chain approach is used. Laddering interviews are conducted with consumers in Norway, Denmark, Hungary and Slovakia.

Findings

Consumers in this study did recognize and appreciate the benefits that HPP and PEF apple juice have to offer over a juice produced by pasteurization. The respondents in all four countries associated positive consequences with product attributes related to the nutritional value and the taste of the products produced by means of these novel technologies. Also the environmental benefits from processing foods by applying these technologies were seen as highly positive characteristics of the technologies. However, many respondents also expressed some scepticism, especially towards the PEF treated juice and were unsure about if there were risks associated with consuming products processed by this technology.

Practical implications

When new processing technologies are introduced, consumer acceptance is one of the key issues for their future success. It is up to food producers and food scientists to provide the evidence that will convince consumers that these new technologies are safe to use.

Originality/value

This research contributes to the limited knowledge on consumer attitudes towards food products produced by HPP and PEF. From a general perspective, the research expands the body of knowledge on consumer perception of food technologies.
Consumer knowledge about dietary fats: another French paradox?
Authors: Saulais Laure , Doyon Maurice , Ruffieux Bernard , Kaiser Harry
Published: January 2012

Purpose

The purpose of this paper is to compare knowledge about dietary fats in some dairy products and other foods across consumers from France, (French‐speaking) Canada and the USA. A relation is explored between the types of information, knowledge levels and obesity predominance.

Design/methodology/approach

A nine‐question nutritional test was developed and administered to three samples of consumers, respectively in Grenoble (France), Quebec, Canada and Ithaca, New York. In France, Canada and the USA the number of participants was respectively 100, 107 and 120. Participants were recruited randomly outside groceries stores and the test was administered directly through one‐on‐one interviews.

Findings

Results indicate a significant gap in knowledge between consumers from the three countries studied. The level and quality of knowledge seems to be correlated with the nature of the informational background: a wider availability of information such as nutrition facts and public health recommendations on fat consumption seems to have a positive effect on the general level of knowledge. However, “technical” knowledge seems to be inversely correlated to the level of obesity.

Research limitations/implications

This work is of an exploratory nature and the sample might not be representative of the countries' population. Further works that link food knowledge and food consumption patterns would be needed.

Practical implications

This study gives weight to the hypothesis that a “science” or nutrient approach to food might not result in appropriate food choices; consumers losing sight of the big picture. To confirm this hypothesis, further work would be needed.

Originality/value

This is, to the authors' knowledge, the first cross‐country study that attempts to link the type of knowledge on fat in food and predominance of obesity. This should encourage nutritionist to further investigate this link. It should also concern the dairy industry, given most often consumers' perception of dairy products' fat content is overestimated, especially for fluid milk in France.
Milk prices in a deregulated market
Authors: Franks Jeremy , Hauser Sarah
Published: January 2012

Purpose

When the UK's Milk Marketing Boards (MMB) were disbanded in 1994 the formal link between the farm gate milk price with the milk's end‐use was broken. The purpose of this paper is to examine whether milk prices fell to their “marginal value in the least remunerative use” or whether “the market had put in place some other mechanism for raising the price upwards”.

Design/methodology/approach

An on‐line survey of UK milk producers, open to all, conducted in the summer of 2008, explored farmers' knowledge of their milk contract, the use of their milk, and the reasons for choosing their current milk buyer.

Findings

A liquid milk price premium (of 1.06ppl.) was earned by farmers who: sold on liquid milk contracts to processors, rather than to one of the three large farmer‐owned co‐operatives; and who recently switched milk buyer. Switching incurred high transaction costs, additional uncertainty, and went against commitments to the co‐operative ideal.

Practical implications

Publication of differences between a buyer's milk price and a benchmark related to how the milk is processed, (a D‐score), cumulative difference values (D_C), 12 and 24 monthly moving average difference measures (D_MA12 and D_MA24 respectively) alongside milk buyers' milk price would improved supply chain transparency, and lower farmers' switching costs. It would also help farmers to treat their milk's final markets, rather than their milk buyer, as their customers.

Originality/value

The paper puts forward practical suggestions that have never been discussed by the UK supply chain, even though they would have direct and indirect benefits to the actors involved.
Museum object as document
Authors: Latham Kiersten F.
Published: January 2012

Purpose

The purpose of this article is to understand the meaning of museum objects from an information perspective. Links are made from Buckland's conceptual information framework as a semiotic to museum object as “document” and finally to user experience of these museum “documents”. The aim is to provide a new lens through which museum studies researchers can understand museum objects and for LIS researchers to accept museum objects as another form of document to be studied.

Design/methodology/approach

A conceptual and comparative analysis of Buckland's information typology as a semiotic. Outcome of analysis forms a model of understanding the museum object as a “document” that is accessed by users on a continuum of experience.

Findings

Michael Buckland's information typology is insightful and useful for a broad understanding of what all heritage institutions have in common: the physical object. Buckland helps us see the museum as an information system, the museum object as a document, and the multidimensional use of the concept information and its semiotic ramifications.

Originality/value

Buckland's typology is important to an understanding of the museum system and museum object in both LIS and museum studies. The concept of “document” opens up a broader perspective, which creates, rather than limits understandings of the human relationship with information. This expanded concept of “document” as sign/semiotic helps us understand user experience in ways not previously explored in the convergence of museums and information studies, from the practical to the theoretical. In this inclusive sense, Buckland's concept of document is a unifying theoretical concept for museums, libraries, and archives.
What is a document institution? A case study from the South Sámi community
Authors: Grenersen Geir
Published: January 2012

Purpose

The Sámis are the indigenous population of Northern Scandinavia. When the oppressive policy against the Sámi population in Norway was lightened during the 1960s, many Sámi communities established language and cultural centers for documentation and development of their language and cultural heritage as the oral tradition lost its ground in the modernization process. This paper aims to discuss how Sámi cultural centers use documentation both as a way of remembering the past and as a political strategy in order to produce evidence for land and water claims.

Design/methodology/approach

The Sámi centers are many‐faceted institutions and document theory is suggested as a theoretical perspective in order to analyze why these institutions were established and how they are functioning today.

Findings

Two cases are presented. The first shows how the centers use documentation as a technique for restoring the past. The second is a ruling in the Norwegian High Court that shows a new turn in what can be accepted as documents proving indigenous land and water claims.

Originality/value

This article is an attempt to introduce document theory as an analytical tool for analyzing the documentation processes in indigenous cultural centers.
Examining thematic elements in strategic business risk
Authors: Ojiako Udechukwu
Published: January 2012

Purpose

The purpose of this paper is exploratory. The author seeks to put forward propositions on how firms may best conceive business risks in an environment characterised by constant change and uncertainty. To construct such a reality, the author examines how the military manages its engagement with strategic risk and uncertainty.

Design/methodology/approach

The paper presents a summated examination of literature published over the last four decades covering three major areas of management literature; risk management, competitive strategy and military tactics are conducted.

Findings

The propositions which are put forward provide the foundation for the empirical development of an appropriate framework for strategic risk management.

Originality/value

The major contribution of the study is that it has focused readers on not only strategic risk and competition, but on how lessons can be drawn from the military's experience of dealing with irregular forms of competition.
Capital structure theory and new technology firms: is there a match?
Authors: Coleman Susan , Robb Alicia
Published: January 2012

Purpose

The purpose of this paper is to explore the extent to which various theories of capital structure “fit” in the case of new technology‐based firms.

Design/methodology/approach

This study uses data from the Kauffman Firm Survey, a longitudinal data set of over 4,000 firms in the USA. Descriptive statistics and multivariate results are provided.

Findings

The authors' findings reveal that new technology‐based firms demonstrate different financing patterns than firms that are not technology‐based.

Research limitations/implications

Although some support was found for both the Pecking Order and Life Cycle theories, the results also indicate that technology‐based entrepreneurs are both willing and able to raise substantial amounts of capital from external sources.

Practical implications

Technology‐based entrepreneurs need external sources of equity, in particular, in order to launch and grow their firms.

Originality/value

To the authors' knowledge, this is the first article to test specific theories of capital structure using a large sample of new technology‐based firms in the USA.