bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of TR4 Orphan Nuclear Receptor Reduces Phosphoenolpyruvate Carboxykinase–Mediated Gluconeogenesis
Authors: Liu Ning-Chun , Lin Wen-Jye , Kim Eungseok , Collins Loretta L. , Lin Hung-Yun , Yu I-Chen , Sparks Janet D. , Chen Lu-Min , Lee Yi-Fen , Chang Chawnshang 
Published: September 2007

OBJECTIVE—Regulation of phosphoenolpyruvate carboxykinase (PEPCK), the key gene in gluconeogenesis, is critical for glucose homeostasis in response to quick nutritional depletion and/or hormonal alteration.
RESEARCH DESIGN/METHODS AND RESULTS— Here, we identified the testicular orphan nuclear receptor 4 (TR4) as a key PEPCK regulator modulating PEPCK gene via a transcriptional mechanism. TR4 transactivates the 490-bp PEPCK promoter-containing luciferase reporter gene activity by direct binding to the TR4 responsive element (TR4RE) located at −451 to −439 in the promoter region. Binding to TR4RE was confirmed by electrophoretic mobility shift and chromatin immunoprecipitation assays. Eliminating TR4 via knockout and RNA interference (RNAi) in hepatocytes significantly reduced the PEPCK gene expression and glucose production in response to glucose depletion. In contrast, ectopic expression of TR4 increased PEPCK gene expression and hepatic glucose production in human and mouse hepatoma cells. Mice lacking TR4 also display reduction of PEPCK expression with impaired gluconeogenesis.
CONCLUSIONS—Together, both in vitro and in vivo data demonstrate the identification of a new pathway, TR4 → PEPCK → gluconeogenesis → blood glucose, which may allow us to modulate metabolic programs via the control of a new key player, TR4, a member of the nuclear receptor superfamily.
Immunohistological evaluation of immune cell infiltrate in cutaneous Kaposi's sarcoma
Authors: Hussein Mahmoud R. 
Published: September 2007

AbstractTypically, Kaposi's sarcoma (KS) also presents with immune cell infiltrates. This study does immunophenotype characterization for demographics of some of these cells to test the hypothesis that ‘development of end‐stage (nodular/tumor) KS is associated with numeric alteration in immune cell infiltrates.’ Fifteen cases of classic‐KS (nodular/tumor) and 20 normal biopsies were examined using antigen‐antibody reactions and immunoperoxidase staining for histiocytes (CD68), B cells (CD20) and T cells (CD3). Variations between normal and lesions were observed with significant increases in immune cell infiltrates (2.3 ± 0.6 vs. 6.4 ± 0.4); CD68+ (4.0 ± 1.0 vs. 7.0 ± 0.5); CD3+ (3.0 ± 1.1 vs. 10.1 ± 0.8); and CD20+ (0.0 ± 0.0 vs. 0.3 ± 0.0). Increased density of immune cells in the nodular lesions of KS may reflect increased antigenicity of these lesions; the increase in T cells suggests enhanced T cell activity in KS. However, these issues should be tested by further studies.
Phenotypically and functionally distinct subsets of natural killer cells in human PBMCs
Authors: Fan Yan‐ying , Yang Bin‐yan , Wu Chang‐you 
Published: September 2007

AbstractHuman natural killer (NK) cells are one major component of lymphocytes that mediate early protection against viruses and tumor cells, and play an important role in immune regulatory functions. In this study, we demonstrated that human NK cells could be divided into four subsets, CD56hiCD16−, CD56loCD16−, CD56+CD16+ and CD56−CD16+, based on the expression of cell surface CD56 and CD16 molecules. Phenotypic analysis of NK cell subsets indicated that the expression of activation markers, adhesion molecules, memory cell markers, inhibitory and activating receptors, and intracellular proteins (granzyme B and perforin) were heterogeneous. Following interleukin (IL)‐2 stimulation, interferon‐γ was preferentially produced by CD56+CD16− NK cells and this subset showed more proliferative capacity. The cytolytic activity of both CD56+CD16− and CD56+/−CD16+ subsets could be augmented in response to IL‐2. The data provided a new definition for NK cell subsets demonstrating their phenotypic and functional diversity and possible stage of NK cell differentiation in peripheral blood.
Antisense oligonucleotide Elk‐1 suppresses the tumorigenicity of human hepatocellular carcinoma cells
Authors: Ying Tsung‐Ho , Hsieh Yi‐Hsien , Hsieh Yih‐Shou , Liu Jer‐Yuh 
Published: September 2007

AbstractIn previous studies, we showed that reducing Ets‐like protein‐1 (Elk‐1) expression inhibited protein kinase C alpha (PKCα) expression and decreased cell migration and invasion in human hepatocellular carcinoma (HCC). In this study, we have investigated the role of Elk‐1 in tumorigenesis. SK‐Hep‐1 HCC cells were transfected with the ElK‐1 antisense oligonucleotide (ODN). In the pretreated cells we detected a reduction of mRNA level using RT—PCR. The inhibitory rate of cell growth was measured by MTT assay. Pretreated‐SK‐Hep‐1 HCC cells were implanted subcutaneously into nude mice to observe the tumor growth and calculate tumor inhibitory rate. The results showed that 5 μM of the antisense ODN Elk‐1 suppressed both Elk‐1 and PKCα production by SK‐Hep‐1 HCC cells after cationic liposome‐mediated transfection, to 8% and 1% of control values, respectively, and the growth of SK‐Hep‐1 HCC cells was inhibited at 2–5 μM doses of the antisense ODN Elk‐1. The control reagent, sense ODN Elk‐1, showed no effects. In BALB/nude mice, SK‐Hep‐1 HCC cells transfected with the 5 μM antisense ODN Elk‐1 formed tumors much smaller than those of sense ODN Elk‐1 pretreated cells. The maximum inhibitory rate of tumor growth was 80.8 ± 12.6% and the tumor formation time was prolonged from 13 to 25 days. These findings suggested the usefulness of antisense ODN Elk‐1 as a new reagent for liver cancer therapy.
Three‐dimensional matrix induces sustained activation of ERK1/2 via Src/Ras/Raf signaling pathway
Authors: Damianova Ralica , Stefanova Nadezhda , Cukierman Edna , Momchilova Albena , Pankov Roumen 
Published: September 2007

AbstractResearch in cell signaling often depends on tissue culture, but the artificial substrates used to grow cellsin vitroare likely to distort the conclusions, particularly when adhesion‐mediated signaling events are investigated. Studies of signal transduction pathways operating in cells grown in three‐dimensional (3D) matrices provide a better system, giving a closer insight of the cell signalingin vivo. We compared the steady‐state levels of ERK1/2 activity in primary human fibroblasts, induced by cell‐derived 3D fibronectin matrix or fibronectin, coated on flat surfaces. 3D environment caused ERK1/2 stimulation concomitant with a 2.5‐fold increase in Ras GTP loading and Src activation. Under these conditions FAK autophosphorylation was suppressed. Treatment with Src inhibitor PP2 abolished these effects indicating that 3D fibronectin matrix activated ERK1/2 through Src/Ras/Raf pathway, bypassing FAK. These observations suggest that withinin vivo‐like conditions Src may have a leading role in the induction of sustained ERK1/2 activation.
TAGster: efficient selection of LD tag SNPs in single or multiple populations
Authors: Xu Zongli , Kaplan Norman L. , Taylor Jack A. 
Published: September 2007

AbstractSummary: Genetic association studies increasingly rely on the use of linkage disequilibrium (LD) tag SNPs to reduce genotyping costs. We developed a software package TAGster to select, evaluate and visualize LD tag SNPs both for single and multiple populations. We implement several strategies to improve the efficiency of current LD tag SNP selection algorithms: (1) we modify the tag SNP selection procedure of Carlson et al. to improve selection efficiency and further generalize it to multiple populations. (2) We propose a redundant SNP elimination step to speed up the exhaustive tag SNP search algorithm proposed by Qin et al. (3) We present an additional multiple population tag SNP selection algorithm based on the framework of Howie et al., but using our modified exhaustive search procedure. We evaluate these methods using resequenced candidate gene data from the Environmental Genome Project and show improvements in both computational and tagging efficiency.Availability: The software Package TAGster is freely available at http://www.niehs.nih.gov/research/resources/software/tagster/Contact: taylor@niehs.nih.govSupplementary information: Additional information, including a tutorial, detailed algorithm and detailed evaluation results, is also available from TAGster web site (see above).
Exploiting sample variability to enhance multivariate analysis of microarray data
Authors: Möller-Levet Carla S. , West Catharine M. , Miller Crispin J. 
Published: September 2007

AbstractMotivation: Biological and technical variability is intrinsic in any microarray experiment. While most approaches aim to account for this variability, they do not actively exploit it. Here, we consider a novel approach that uses the variability between arrays to provide an extra source of information that can enhance gene expression analyses.Results: We develop a method that uses sample similarity to incorporate sample variability into the analysis of gene expression profiles. This allows each pairwise correlation calculation to borrow information from all the data in the experiment. Results on synthetic and human cancer microarray datasets show that the inclusion of this information leads to a significant increase in the ability to identify previously characterized relationships and a reduction in false discovery rate, when compared to a standard analysis using Pearson correlation. The information carried by the variability between arrays can be exploited to significantly improve the analysis of gene expression data.Availability: Matlab script files are available from the author.Contact: cmoller@picr.man.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
Modeling protein loops with knowledge-based prediction of sequence-structure alignment
Authors: Peng Hung-Pin , Yang An-Suei 
Published: September 2007

AbstractMotivation: As protein structure database expands, protein loop modeling remains an important and yet challenging problem. Knowledge-based protein loop prediction methods have met with two challenges in methodology development: (1) loop boundaries in protein structures are frequently problematic in constructing length-dependent loop databases for protein loop predictions; (2) knowledge-based modeling of loops of unknown structure requires both aligning a query loop sequence to loop templates and ranking the loop sequence-template matches.Results: We developed a knowledge-based loop prediction method that circumvents the need of constructing hierarchically clustered length-dependent loop libraries. The method first predicts local structural fragments of a query loop sequence and then structurally aligns the predicted structural fragments to a set of non-redundant loop structural templates regardless of the loop length. The sequence-template alignments are then quantitatively evaluated with an artificial neural network model trained on a set of predictions with known outcomes. Prediction accuracy benchmarks indicated that the novel procedure provided an alternative approach overcoming the challenges of knowledge-based loop prediction.Availability: http://cmb.genomics.sinica.edu.twContact: yangas@gate.sinica.edu.twSupplementary information: Supplementary data are available at Bioinformatics online.
The Role of Phosphoenolpyruvate Carboxylase during C4 Photosynthetic Isotope Exchange and Stomatal Conductance
Authors: Cousins Asaph B. , Baroli Irene , Badger Murray R. , Ivakov Alexander , Lea Peter J. , Leegood Richard C. , von Caemmerer Susanne 
Published: September 2007

Abstract
Phosphoenolpyruvate carboxylase (PEPC; EC 4.1.1.31) plays a key role during C4 photosynthesis and is involved in anaplerotic metabolism, pH regulation, and stomatal opening. Heterozygous (Pp) and homozygous (pp) forms of a PEPC-deficient mutant of the C4 dicot Amaranthus edulis were used to study the effect of reduced PEPC activity on CO2 assimilation rates, stomatal conductance, and 13CO2 (Δ13C) and C18OO (Δ18O) isotope discrimination during leaf gas exchange. PEPC activity was reduced to 42% and 3% and the rates of CO2 assimilation in air dropped to 78% and 10% of the wild-type values in the Pp and pp mutants, respectively. Stomatal conductance in air (531 μbar CO2) was similar in the wild-type and Pp mutant but the pp mutant had only 41% of the wild-type steady-state conductance under white light and the stomata opened more slowly in response to increased light or reduced CO2 partial pressure, suggesting that the C4 PEPC isoform plays an essential role in stomatal opening. There was little difference in Δ13C between the Pp mutant (3.0‰ ± 0.4‰) and wild type (3.3‰ ± 0.4‰), indicating that leakiness (ϕ), the ratio of CO2 leak rate out of the bundle sheath to the rate of CO2 supply by the C4 cycle, a measure of the coordination of C4 photosynthesis, was not affected by a 60% reduction in PEPC activity. In the pp mutant Δ13C was 16‰ ± 3.2‰, indicative of direct CO2 fixation by Rubisco in the bundle sheath at ambient CO2 partial pressure. Δ18O measurements indicated that the extent of isotopic equilibrium between leaf water and the CO2 at the site of oxygen exchange (θ) was low (0.6) in the wild-type and Pp mutant but increased to 0.9 in the pp mutant. We conclude that in vitro carbonic anhydrase activity overestimated θ as compared to values determined from Δ18O in wild-type plants.
A Central Role of Abscisic Acid in Drought Stress Protection of Agrobacterium-Induced Tumors on Arabidopsis
Authors: Efetova Marina , Zeier Jürgen , Riederer Markus , Lee Chil-Woo , Stingl Nadja , Mueller Martin , Hartung Wolfram , Hedrich Rainer , Deeken Rosalia 
Published: September 2007

Abstract
Crown gall tumors induced by Agrobacterium tumefaciens represent a sink that has to be provided with nutrients and water by the host plant. The lack of an intact epidermis or cuticle results in uncontrolled loss of water. However, neither the tumor nor the host plant displays wilting. This phenomenon points to drought adaptation in both tumors and the crown gall host plant. To understand the underlying molecular mechanisms of protection against desiccation the gene expression pattern of Arabidopsis (Arabidopsis thaliana) tumors was integrated with the profile of stress metabolites: Arabidopsis tumors accumulated high amounts of abscisic acid (ABA), the ethylene precursor aminocyclopropyl carboxylic acid, osmoprotectants, and form a suberized periderm-like protective layer. Suberization of the outer tumor cell layers most likely is mediated by ABA since external application of ABA induced suberization of Arabidopsis roots. However, the expression level of the classical marker genes, known to respond to drought stress and/or ABA, was lower in tumors. Instead another set of drought and/or ABA-inducible genes was more highly transcribed. Elevated transcription of several ABA-dependent aquaporin genes might indicate that ABA controls the water balance of the tumor. The retarded tumor growth on abi and aba mutant plants underlined the importance of a tumor-specific ABA signaling pathway. Taken together, we propose that ABA is an important signal for protection of tumors against desiccation and thus supports tumor development.
AP2-ERF Transcription Factors Mediate Nod Factor–Dependent MtENOD11Activation in Root Hairs via a Novelcis-Regulatory Motif
Authors: Andriankaja Andry , Boisson-Dernier Aurélien , Frances Lisa , Sauviac Laurent , Jauneau Alain , Barker David G. , de Carvalho-Niebel Fernanda 
Published: September 2007

AbstractRhizobium Nod factors (NFs) are specific lipochitooligosaccharides that activate host legume signaling pathways essential for initiating the nitrogen-fixing symbiotic association. This study describes the characterization of cis-regulatory elements and trans-interacting factors that regulate NF-dependent and epidermis-specific gene transcription in Medicago truncatula. Detailed analysis of the Mt ENOD11 promoter using deletion, mutation, and gain-of-function constructs has led to the identification of an NF-responsive regulatory unit (the NF box) sufficient to direct NF-elicited expression in root hairs. NF box–mediated expression requires a major GCC-like motif, which is also essential for the binding of root hair–specific nuclear factors. Yeast one-hybrid screening has identified three closely related AP2/ERF transcription factors (ERN1 to ERN3) that are able to bind specifically to the NF box. ERN1 is identical to an ERF-like factor identified recently. Expression analysis has revealed that ERN1 and ERN2 genes are upregulated in root hairs following NF treatment and that this activation requires a functional NFP gene. Transient expression assays in Nicotiana benthamiana have further shown that nucleus-targeted ERN1 and ERN2 factors activate NF box–containing reporters, whereas ERN3 represses ERN1/ERN2-dependent transcription activation. A model is proposed for the fine-tuning of NF-elicited gene transcription in root hairs involving the interplay between repressor and activator ERN factors.
Information Science at City University London
Authors: Bawden David 
Published: September 2007

PurposeThe paper seeks to introduce a special issue of Aslib Proceedings, which contains a series of papers written by staff and research students at the Department of Information Science, City University London.Design/methodology/approachThis introductory paper introduces the other papers in the special issue and sets them in context.FindingsThis editorial argues that the information science discipline, which has always been the focus of City's research and scholarship, is a valid academic discipline with a positive future.Originality/valueThe paper points out the particular strengths and historical continuity of the City Information Science Department.
Flickr and Democratic Indexing: dialogic approaches to indexing
Authors: Rafferty Pauline , Hidderley Rob 
Published: September 2007

PurposeThe purpose of this paper is two‐fold: to examine three models of subject indexing (i.e. expert‐led indexing, author‐generated indexing, and user‐orientated indexing); and to compare and contrast two user‐orientated indexing approaches (i.e. the theoretically‐based Democratic Indexing project, and Flickr, a working system for describing photographs).Design/methodology/approachThe approach to examining Flickr and Democratic Indexing is evaluative. The limitations of Flickr are described and examples are provided. The Democratic Indexing approach, which the authors believe offers a method of marshalling a “free” user‐indexed archive to provide useful retrieval functions, is described.FindingsThe examination of both Flickr and the Democratic Indexing approach suggests that, despite Shirky's claim of philosophical paradigm shifting for social tagging, there is a residing doubt amongst information professionals that self‐organising systems can work without there being some element of control and some form of “representative authority”.Originality/valueThis paper contributes to the literature of user‐based indexing and social tagging.
Corrosion of chromate conversion films on aluminium in electrically bonded interfaces
Authors: Shoja Razavi Reza 
Published: September 2007

PurposeThe present study aims to investigate the corrosion and electrical properties of the chromate conversion coatings on aluminium alloy Type 6061 in electrically bonded interfaces.Design/methodology/approachTests were carried out to obtain the optimum conditions for chromate bath composition and immersion time for standard requirement provisions such as corrosion resistance in the salt‐spray test, electrical resistance and coating quality. The applied coatings were tested electrochemically in seawater and distilled water. The protection mechanism was evaluated from Tafel and cyclic polarisation curves in the said environments.FindingsThe evaluations showed that the passive film layer contained chromate with alumina formed on the substrate. The good performance of the conversion coating in terms of its corrosion and electrical conductivity was probably due to the characteristics of this protective film.Originality/valueThe paper presents findings on the corrosion of chromate conversion films on aluminium in electrically bonded interfaces.
Corrosion inhibition of copper in sulphuric acid by some nitrogen heterocyclic compounds
Authors: Shahrabi T. , Tavakholi Hossein , Hosseini M.G. 
Published: September 2007

PurposeIn this paper, the main aim is to study the influence of some nitrogen heterocyclic compounds, namely 2‐mercaptobenzimidazole (2‐MBI), 2‐mercaptobenzoxazole (2‐MBO) and 2‐mercaptobenzothiazole (2‐MBT) on the corrosion inhibition of copper in 0.5 M sulphuric acid.Design/methodology/approachMeasurements were carried out in a three‐electrode cell that was connected to the corrosion measurement system using software for Tafel polarization. Impedance measurements were carried out at open circuit potential using an electrochemical interface and frequency response analyzer at frequencies from 100 kHz to 10 MHz.FindingsFor all the compounds, a consistent trend of increase in inhibition efficiency was observed as a function of concentration. The adsorption of all the compounds on to the copper surface in the acidic solution was found to obey the Langmuir Adsorption Isotherm. The values of activation energy and free energy of adsorption for all the compounds also were calculated. The Tafel polarization studies indicated that all the compounds were mixed inhibitors.Research limitations/implicationsIn order to further the performance of heterocyclic compounds and also to identify their synergistic effects with some additives (such as surfactants) it is suggested that further research into the behaviour of these heterocyclic compounds with other metals be carried out.Originality/valueThe results of this paper can be used for acid descaling of copper in which suitable inhibitor systems with the highest efficiencies are required.
Making sense of blended learning
Authors: Sloman Martyn 
Published: September 2007

PurposeThis paper has the aim of considering blended learning in the global context.Design/methodology/approachThe approach is to use research surveys supplemented by extensive case study interviews involving 19 countriesFindingsThe paper finds that it seems beyond doubt that the concept of blended learning has arrived and is here to stay. However, if it is to add value to our understanding of effective training and learning the term needs to be considered in a broader context. It is not simply about delivery and technology. If the term blended learning is to have longevity in our trainer vocabulary we must extend its use beyond technology. It must be as much about varying learning methodology as it is about training delivery. We must understand more about what motivates learners, what support they need and how these supportive interventions can take place in practice. Only with this understanding can we get the “blend” right.Practical implicationsEmphasis needs to be shifted from technology to learning.Originality/valueThe paper includes a case study based on language training in India using a blended approach.