bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Risk Factors for Bleeding After Liver Biopsy in Children
Authors: Westheim Birgitte H. , Østensen Anniken B. , Aagenæs Ingegerd , Sanengen Truls , Almaas Runar 
Published: January 2012

ABSTRACTObjectives:Acetylsalicylic acid is used in liver‐transplanted children to prevent thrombosis of the hepatic artery. We evaluated whether acetylsalicylic acid and other risk factors were associated with bleeding after percutaneous liver biopsy.Methods:Medical charts, laboratory results, imaging studies, and anesthesia charts of 275 ultrasound‐guided liver biopsy procedures in 190 children were reviewed. A total of 178 biopsies were performed on native livers and 97 on transplanted livers.Results:Three major and 28 minor bleeding incidents were found. The mortality rate was 0%. Acetylsalicylic acid had been given the last 5 days before 55 of the biopsy procedures and no increased risk of bleeding was found (odds ratio 0.96 [0.37–2.26]; P = 1.00). Low‐molecular‐weight heparin and biopsies from focal lesions were risk factors for bleeding complications. Acute liver failure was associated with increased risk for major complications (odds ratio 26.1 [3.3–205]; P = 0.01) and was a risk factor for major bleeding. Postbiopsy ultrasound the day after the procedure (n = 266 [96% of 275 biopsies]) revealed minor bleeding after 7.1% of the biopsies and after 2.6% of the ultrasounds revealed unsuspected bleeding, but none of these required intervention.Conclusions:Ultrasound‐guided liver biopsy in children is a procedure with a low rate of major complications and a high rate of minor bleeding not requiring intervention. Treatment with low‐dose acetylsalicylic acid did not increase bleeding incidence or total complication rate. Low‐molecular‐weight heparin and biopsies from focal lesions were risk factors for bleeding complications. Routine ultrasound the day after the procedure did not change handling of the patients.
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

AbstractThe 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

Abstract
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

AbstractDespite 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

Abstract
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

Abstract
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

Abstract
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

PurposeThe 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/approachRedalyc 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.FindingsThe 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/valueThe 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

PurposeScholarly 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/approachThe 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.FindingsThe 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/valueThis 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

PurposeThis 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/approachOntOAIr uses simplified document representations, a clustering algorithm, and ontological engineering techniques.FindingsThe 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/implicationsBy 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/valueThe 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

PurposeThis 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/approachThe 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.FindingsResults 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/valueThis 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

PurposeThe 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/approachA 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.FindingsThe 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/implicationsThe 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 implicationsThe 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/valueTo 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

PurposeThe 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/approachThis 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.FindingsThe 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 implicationsThe 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/valueThis 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.