bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality of information accompanying on-line marketing of home diagnostic tests
Authors: Datta Adrija K , Selman Tara J , Kwok Tony , Tang Teresa , Khan Khalid S 
Published: February 2008

Objective To assess the quality of information provided to consumers by websites marketing medical home diagnostic tests. Design A cross-sectional analysis of a database developed from searching targeted websites. Setting Data sources were websites written in English which marketed medical home diagnostic tests. Main outcome measures A meta-search engine was used to identify the first 20 citations for each type of home diagnostic medical test. Relevant websites limited to those written in English were reviewed independently and in triplicate, with disputes resolved by two further reviewers. Information on the quality of these sites was extracted using a pre-piloted performer. Results 168 websites were suitable for inclusion in the review. The quality of these sites showed marked variation. Only 24 of 168 (14.2%) complied with at least three-quarters of the quality items and just over half (95 of 168, 56.5%) reported official approval or certification of the test. Information on accuracy of the test marketed was reported by 87 of 168 (51.7%) websites, with 15 of 168 (8.9%) providing a scientific reference. Instructions for use of the product were found in 97 of 168 (57.9%). However, the course of action to be taken after obtaining the test result was stated in only 63 of 168 (37.5%) for a positive result and 43 of 168 (25.5%) for a negative result. Conclusions The quality of information posted on commercial websites marketing home tests online is unsatisfactory and potentially misleading for consumers.
Three distinct neuroprotective functions of myricetin against glutamate‐induced neuronal cell death: Involvement of direct inhibition of caspase‐3
Authors: Shimmyo Yoshiari , Kihara Takeshi , Akaike Akinori , Niidome Tetsuhiro , Sugimoto Hachiro 
Published: February 2008

AbstractThe excitatory neurotransmitter glutamate can accumulate in the brain and is thought to be involved in the etiology of many neurodegenerative disorders, including ischemia and Alzheimer disease. Therefore, it is important to search for compounds that reduce glutamate neurotoxicity. This glutamate‐mediated excitotoxicity is caused by intracellular Ca2+overload via the N‐methyl‐D‐aspartate receptor NMDAR), reactive oxygen species (ROS) generation, and caspase‐3 activation. Here we show that the natural flavonoid myricetin inhibited glutamate‐induced excitotoxicity and protected neurons by multiple, distinct pathways. First, myricetin affected modulation of the NMDAR by phosphorylation, causing a subsequent reduction in glutamate‐induced intracellular Ca2+overload. Second, myricetin inhibited the ROS production caused by glutamate. Finally, glutamate‐induced activation of caspase‐3 was reduced by myricetin treatment. Moreover, myricetin directly interacted with the active site of caspase‐3 via three hydrogen bonds and inhibited its activity. We conclude that myricetin inhibited glutamate‐induced neuronal toxicity by multiple biochemical pathways. These results show that myricetin is a potent antineurodegenerative compound and may contribute to the discovery of a drug with which to combat neurodegeneration. © 2008 Wiley‐Liss, Inc.
Neuroprotective effects of SB‐415286 on hydrogen peroxide‐induced cell death in B65 rat neuroblastoma cells and neurons
Authors: Pizarro Javier G. , Yeste‐Velasco Marc , Rimbau Victor , Casadesús Gemma , Smith Mark A. , Pallàs Mercè , Folch Jaume , Camins Antoni 
Published: February 2008

AbstractGlycogen synthase kinase‐3 (GSK‐3) is involved in the pathogenesis of several neurodegenerative diseases. In addition, as oxidative stress has been implicated in all neurodegenerative disorders, the inhibition of both pathways offers a potential strategy for preventing or delaying neurodegeneration. We examined the cytoprotective effects of lithium and SB‐415286, two inhibitors of GSK‐3, using a rat B65 cell line and also in cerebellar granule cells (CGN). H2O2 decreased the inactive form of GSK‐3 (phospho‐GSK‐3 at Ser9), as measured by immunoblot experiments involving an antibody against the inactive form of the enzyme. Moreover, lithium inhibited this effect. While SB‐415286 exerted a protective effect, lithium did not attenuate the toxic effects of H2O2 (1 mM). We then examined those mechanisms implicated in the protective effects of SB‐415286. When we analyzed reactive oxygen species (ROS) production using the fluorescent probe 2,7‐dichlorodihydrofluorescein diacetate in B65 cells, as well as in CGN, we found that SB‐415286 strongly reduced DCF fluorescence. Lithium, however, did not exhibit any antioxidant properties. We conclude that the GSK‐3 inhibitor SB‐415286 has antioxidant properties, which may explain the cytoprotective effects against H2O2 damage. Furthermore, inhibition of GSK‐3 activity was not involved in this protective effect.
Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes
Authors: Lee Hyunju , Kong Sek Won , Park Peter J. 
Published: February 2008

Abstract
Motivation: DNA copy number aberrations (CNAs) and gene expression (GE) changes provide valuable information for studying chromosomal instability and its consequences in cancer. While it is clear that the structural aberrations and the transcript levels are intertwined, their relationship is more complex and subtle than initially suspected. Most studies so far have focused on how a CNA affects the expression levels of those genes contained within that CNA.
Results: To better understand the impact of CNAs on expression, we investigated the correlation of each CNA to all other genes in the genome. The correlations are computed over multiple patients that have both expression and copy number measurements in brain, bladder and breast cancer data sets. We find that a CNA has a direct impact on the gene amplified or deleted, but it also has a broad, indirect impact elsewhere. To identify a set of CNAs that is coordinately associated with the expression changes of a set of genes, we used a biclustering algorithm on the correlation matrix. For each of the three cancer types examined, the aberrations in several loci are associated with cancer-type specific biological pathways that have been described in the literature: CNAs of chromosome (chr) 7p13 were significantly correlated with epidermal growth factor receptor signaling pathway in glioblastoma multiforme, chr 13q with NF-kappaB cascades in bladder cancer, and chr 11p with Reck pathway in breast cancer. In all three data sets, gene sets related to cell cycle/division such as M phase, DNA replication and cell division were also associated with CNAs. Our results suggest that CNAs are both directly and indirectly correlated with changes in expression and that it is beneficial to examine the indirect effects of CNAs.
Availability: The code is available upon request.
Contact: peter_park@harvard.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Interactive visualization software for exploring phylogenetic trees and clades
Authors: Derthick Mark 
Published: February 2008

Abstract
Summary: The Summary Tree Explorer (STE) is a Java application for interactively exploring sets of phylogenetic trees using two coupled representations: a node-and-link diagram and a textual list of common clades. Selection, pruning, filtering or re-rooting in one representation is immediately reflected in the other. While summary trees are more effective at showing the relationship among clades, they can only show a consistent subset of those that appear in the textual list. Working with both representations mitigates the disadvantages of having to choose just one.
Availability: STE, along with several sample datasets, is available at http://cityscape.inf.cs.cmu.edu/phylogeny/
Contact: mad@cs.cmu.edu
Statistical search on the Semantic Web
Authors: Kobayashi Norio , Toyoda Tetsuro 
Published: February 2008

Abstract
Motivation: Statistical analysis of links on the Semantic Web is important for various evaluation purposes such as quantifying an individual's scientific research output based on citation links. SPARQL has been proposed as a standardized query language for the Semantic Web and is intuitively understandable; however, it does not adequately support statistical evaluation of semantic links.
Results: We have extended SPARQL to a novel Resource Description Framework (RDF) query language termed General and Rapid Association Study Query Language (GRASQL) to generate inferences connecting semantic Boolean-based deduction and statistical evaluation of RDF resources. We have verified the descriptive capability of GRASQL by writing GRASQL queries for practical biomedical search patterns including in silico positional cloning studies and for ranking researchers in a specific domain of expertise by introducing k index, the number of papers containing specific keywords that are published in a fixed period by a researcher. We have also developed a search engine termed General and Rapid Association Study Engine (GRASE), which executes a restricted variety of GRASQL queries by requesting a dynamic and comprehensive evaluation of statistical significance of intersections between each group of documents assigned to URIs and those documents matching user-specified keywords and omics conditions. By performing practical in silico positional cloning searches with GRASE, we show the relevance of our approach on the Semantic Web for biomedical knowledge discovery problem solving.
Availability: GRASE is used as the search engine for the Positional Medline (PosMed) service and Researcher Finder service at http://omicspace.riken.jp/
Contact: toyop@gsc.riken.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
New Connections across Pathways and Cellular Processes: Industrialized Mutant Screening Reveals Novel Associations between Diverse Phenotypes in Arabidopsis
Authors: Lu Yan , Savage Linda J. , Ajjawi Imad , Imre Kathleen M. , Yoder David W. , Benning Christoph , DellaPenna Dean , Ohlrogge John B. , Osteryoung Katherine W. , Weber Andreas P. , Wilkerson Curtis G. , Last Robert L. 
Published: February 2008

AbstractIn traditional mutant screening approaches, genetic variants are tested for one or a small number of phenotypes. Once bona fide variants are identified, they are typically subjected to a limited number of secondary phenotypic screens. Although this approach is excellent at finding genes involved in specific biological processes, the lack of wide and systematic interrogation of phenotype limits the ability to detect broader syndromes and connections between genes and phenotypes. It could also prevent detection of the primary phenotype of a mutant. As part of a systems biology approach to understand plastid function, large numbers of Arabidopsis thaliana homozygous T-DNA lines are being screened with parallel morphological, physiological, and chemical phenotypic assays (www.plastid.msu.edu). To refine our approaches and validate the use of this high-throughput screening approach for understanding gene function and functional networks, approximately 100 wild-type plants and 13 known mutants representing a variety of phenotypes were analyzed by a broad range of assays including metabolite profiling, morphological analysis, and chlorophyll fluorescence kinetics. Data analysis using a variety of statistical approaches showed that such industrial approaches can reliably identify plant mutant phenotypes. More significantly, the study uncovered previously unreported phenotypes for these well-characterized mutants and unexpected associations between different physiological processes, demonstrating that this approach has strong advantages over traditional mutant screening approaches. Analysis of wild-type plants revealed hundreds of statistically robust phenotypic correlations, including metabolites that are not known to share direct biosynthetic origins, raising the possibility that these metabolic pathways have closer relationships than is commonly suspected.
Analysis of Protein Complexes in Wheat Amyloplasts Reveals Functional Interactions among Starch Biosynthetic Enzymes
Authors: Tetlow Ian J. , Beisel Kim G. , Cameron Scott , Makhmoudova Amina , Liu Fushan , Bresolin Nicole S. , Wait Robin , Morell Matthew K. , Emes Michael J. 
Published: February 2008

Abstract
Protein-protein interactions among enzymes of amylopectin biosynthesis were investigated in developing wheat (Triticum aestivum) endosperm. Physical interactions between starch branching enzymes (SBEs) and starch synthases (SSs) were identified from endosperm amyloplasts during the active phase of starch deposition in the developing grain using immunoprecipitation and cross-linking strategies. Coimmunoprecipitation experiments using peptide-specific antibodies indicate that at least two distinct complexes exist containing SSI, SSIIa, and either of SBEIIa or SBEIIb. Chemical cross linking was used to identify protein complexes containing SBEs and SSs from amyloplast extracts. Separation of extracts by gel filtration chromatography demonstrated the presence of SBE and SS forms in protein complexes of around 260 kD and that SBEII forms may also exist as homodimers. Analysis of cross-linked 260-kD aggregation products from amyloplast lysates by mass spectrometry confirmed SSI, SSIIa, and SBEII forms as components of one or more protein complexes in amyloplasts. In vitro phosphorylation experiments with γ-32P-ATP indicated that SSII and both forms of SBEII are phosphorylated. Treatment of the partially purified 260-kD SS-SBE complexes with alkaline phosphatase caused dissociation of the assembly into the respective monomeric proteins, indicating that formation of SS-SBE complexes is phosphorylation dependent. The 260-kD SS-SBEII protein complexes are formed around 10 to 15 d after pollination and were shown to be catalytically active with respect to both SS and SBE activities. Prior to this developmental stage, SSI, SSII, and SBEII forms were detectable only in monomeric form. High molecular weight forms of SBEII demonstrated a higher affinity for in vitro glucan substrates than monomers. These results provide direct evidence for the existence of protein complexes involved in amylopectin biosynthesis.
BRICK1 Is Required for Apical Cell Growth in Filaments of the MossPhyscomitrella patensbut Not for Gametophore Morphology
Authors: Perroud Pierre-François , Quatrano Ralph S. 
Published: February 2008

AbstractWhen BRK1, a member of the Wave/SCAR complex, is deleted in Physcomitrella patens (Δbrk1), we report a striking reduction of filament growth resulting in smaller and fewer cells with misplaced cross walls compared with the normal protonemal cells. Using an inducible green fluorescent protein–talin to detect actin in living tissue, a characteristic broad accumulation of actin is observed at the tip of wild-type apical cells, whereas in Δbrk1, smaller, more distinct foci of actin are present. Insertion of brk1-yfp into Δbrk1 rescues the mutant phenotype and results in BRK1 being localized only in the tip of apical cells, the exclusive site of cell extension and division in the filament. Like BRK1, ARPC4 and At RABA4d are normally localized at the tip of apical cells and their localization is correlated with rapid tip growth in filaments. However, neither marker accumulates in apical cells of Δbrk1 filaments. Although the Δbrk1 phenotypes in protonema are severe, the leafy shoots or gametophores are normally shaped but stunted. These and other results suggest that BRK1 functions directly or indirectly in the selective accumulation/stabilization of actin and other proteins required for polar cell growth of filaments but not for the basic structure of the gametophore.
A LysM Receptor-Like Kinase Plays a Critical Role in Chitin Signaling and Fungal Resistance inArabidopsis
Authors: Wan Jinrong , Zhang Xue-Cheng , Neece David , Ramonell Katrina M. , Clough Steve , Kim Sung-yong , Stacey Minviluz G. , Stacey Gary 
Published: February 2008

AbstractChitin, a polymer of N-acetyl-d-glucosamine, is found in fungal cell walls but not in plants. Plant cells can perceive chitin fragments (chitooligosaccharides) leading to gene induction and defense responses. We identified a LysM receptor-like protein (LysM RLK1) required for chitin signaling in Arabidopsis thaliana. The mutation in this gene blocked the induction of almost all chitooligosaccharide-responsive genes and led to more susceptibility to fungal pathogens but had no effect on infection by a bacterial pathogen. Additionally, exogenously applied chitooligosaccharides enhanced resistance against both fungal and bacterial pathogens in the wild-type plants but not in the mutant. Together, our data indicate that LysM RLK1 is essential for chitin signaling in plants (likely as part of the receptor complex) and is involved in chitin-mediated plant innate immunity. The LysM RLK1-mediated chitin signaling pathway is unique, but it may share a conserved downstream pathway with the FLS2/flagellin- and EFR/EF-Tu–mediated signaling pathways. Additionally, our work suggests a possible evolutionary relationship between the chitin and Nod factor perception mechanisms due to the similarities between their potential receptors and between the signal molecules perceived by them.
MAP65-3 Microtubule-Associated Protein Is Essential for Nematode-Induced Giant Cell Ontogenesis inArabidopsis
Authors: Caillaud Marie-Cécile , Lecomte Philippe , Jammes Fabien , Quentin Michaël , Pagnotta Sophie , Andrio Emilie , de Almeida Engler Janice , Marfaing Nicolas , Gounon Pierre , Abad Pierre , Favery Bruno 
Published: February 2008

AbstractThe infection of plants by obligate parasitic nematodes constitutes an interesting model for investigating plant cytoskeleton functions. Root knot nematodes have evolved the ability to manipulate host functions to their own advantage by redifferentiating root cells into multinucleate and hypertrophied feeding cells. These giant cells result from repeated rounds of karyokinesis without cell division. Detailed functional analyses demonstrated that Arabidopsis thaliana Microtubule-Associated Protein65-3 (MAP65-3) was essential for giant cell ontogenesis and that cytokinesis was initiated but not completed in giant cells. In developing giant cells, MAP65-3 was associated with a novel kind of cell plate—the giant cell mini cell plate—that separates daughter nuclei. In the absence of functional MAP65-3, giant cells developed but failed to fully differentiate and were eventually destroyed. These defects in giant cells impaired the maturation of nematode larvae. Thus, MAP65-3 is essential for giant cell development during root knot nematode infection. Subcellular localization of MAP65-3 and analysis of microtubule organization in the dyc283 T-DNA map65-3 mutant demonstrated that MAP65-3 played a critical role in organizing the mitotic microtubule array during both early and late mitosis in all plant organs. Here, we propose a model for the role of MAP65-3 in giant cell ontogenesis.
Changes in anti‐nutritional factors in Indian bean (Dolichos lablabL.) seeds during germination and their behaviour during cooking
Authors: Ramakrishna V. , Jhansi Rani P. , Ramakrishna Rao P. 
Published: February 2008

PurposeThis paper aims to study the changes in anti‐nutritional factors during the germination of the Indian bean and also to carryout an evaluation by subjecting it to different cooking treatments – boiling, roasting and pressure cooking.Design/methodology/approachThe healthy Indian bean (Dolichos lablabL.) seeds were soaked for 12 h and allowed to germinate (sprout) at room temperature 27±2○C for a period of 32 h. Seedlings were withdrawn at designated time intervals and used for analysis of anti‐nutritional factors like trypsin inhibitory activity (TIA), phytic acid, polyphenols and tannins of dried and germinated cotyledons. They were also evaluated regarding their changes by subjecting to different cooking treatments – boiling, roasting and pressure cooking.FindingsThe raw dry Indian bean had a very high TIA which decreases progressively to 17 per cent at 32 h germination period. An overall fall in polyphenols of 70 per cent, tannins 46 per cent, phytic acids 36 per cent and phytate phosphorus to 30 per cent was noticed during the 32 h germination period. Maximum reduction was observed in TIA and phytic acids with roasting, while the boiling and pressure cooking decreases the levels of polyphenols and tannins.Originality/valueThe paper proves that germination is a more effective method in reducing TIA, tannins, polyphenols and phytic acid than the various cooking treatments.
“Scores on Doors”: hygiene disclosure schemes for consumers
Authors: Worsfold Denise , Worsfold Philip Mark 
Published: February 2008

PurposeThe purpose of this paper is to determine the utility to consumers of hygiene disclosure schemes for eating places.Design/methodology/approachA sample of hygiene disclosure schemes operated by local authorities in the UK was examined for features that might be expected to influence consumer awareness and behaviour.FindingsThe survey revealed that schemes differed in the interpretation of scores, the extent of information disclosed, the communication channels used to disclose information and the amount of publicity provided for businesses and the public. The majority of schemes provide certificates which businesses are encouraged to display prominently. Hygiene inspection information is posted on the web sites of all the local authorities.Research limitations/implicationsThe number of schemes in this study was limited. A comprehensive evaluation of the current UK “Scores on Doors” schemes will have to take into account a large number of schemes with a very large number of variables, making its feasibility questionable.Practical implicationsThe “Scores on Doors” schemes will only be successful if the public are fully aware of them and the schemes are well respected. They will have to be well publicised, to operate in an open, transparent manner and be consistent and fair. This study shows that, although the schemes have some features in common, there is considerable lack of consistency, particularly in the representation of scores as symbols.Originality/valuePublished evaluations of hygiene disclosure schemes relate to schemes operating outside the UK. This study examines some of the features of current UK schemes that will require consideration if a consistent nation‐wide scheme is to be developed.
Hawker food industry: food safety/public health strategies in Malaysia
Authors: Pang Fiona , See Toh Poh 
Published: February 2008

PurposeThe purpose of this paper is to explore the socio‐demographic factors affecting food safety knowledge/practice and the effectiveness of food safety strategies of hawkers in an urban and less urban setting of Malaysia.Design/methodology/approachA total of 50 hawkers from Kuala Lumpur and Taiping were given a questionnaire and observed in their food safety practice (FSP). In‐depth interviews were performed on four hawkers from Kuala Lumpur and Taiping.Practical implicationsOf all hawker types, Muslim/Malay hawkers, hawkers with higher educational levels, hawkers in designated sites and hawkers in an urban setting scored the highest on food safety knowledge and/or practice. This study found inadequate distribution/impracticality of regulations/guidelines for hawkers, ambiguities with licensing procedures, weaknesses in training programmes and significant complaints of designated sites by hawkers.Originality/valueEthnicity, religion, education and type of premise are socio‐demographic factors that may affect food safety knowledge/practices of hawkers. An urban/less urban setting may also affect hawkers' food safety knowledge/practice. Ineffectiveness of food safety strategies of the Control Authority may exist and may vary across different regions of Malaysia. Thus, food safety strategies must be regulated/reinforced and adapted to hawkers' socio‐demographic status, to ensure the safety of hawker foods in Malaysia.