bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hyperglycemia Stimulates a Sustained Increase in Hydraulic Conductivity In Vivo without Any Change in Reflection Coefficient
Authors: PERRIN RACHEL M. , HARPER STEVEN J. , CORRALL ROGER , BATES DAVID O. 
Published: September 2007

ABSTRACTObjective: Increased microvascular permeability contributes to the development of diabetic microvascular complications and diabetic vasculopathy is correlated with blood glucose levels. The mechanisms underlying increased permeability, however, are poorly understood.Methods: The Landis‐Michel technique was used to measure water permeability (hydraulic conductivity, Lp) and macromolecular permeability (reflection coefficient, σ) of exchange capillaries in frogs and rats.Results: Dialysed normoglycemic plasma from diabetic patients had no effect on Lp. The same plasma with 20 mM glucose increased hydraulic conductivity from (mean ± SEM × 10−7 cm · s−1· cm H2O–1) 5.73 ± 2.01 to 13.09 ± 2.67 (P < .01). Nondiabetic control plasma did not affect Lp, but addition of 20 mM glucose increased Lp to a similar degree. The effect of glucose alone was examined. Glucose at 20 mM increased Lp, from 2.82 ± 0.61 to 4.71 ± 1.35 × 10− 7 cm · s− 1· cm H2O–1 (P = .002, n = 13). A similar increase was seen in rat mesenteric microvessels, from 1.04 ± 0.40 in control perfusions to 2.18 ± 0.56, P < .05. The microvascular macromolecular reflection coefficient in all the above experiments was unaltered. The use of specific inhibitors indicated that the glucose‐induced increased Lp did not appear to be mediated through protein kinase C (PKC), free radical generation, glucose metabolism, or albumin glycation.Conclusions: These data suggest that hyperglycemia induced increased apparent protein permeability may be secondary to a glucose‐mediated change in macromolecular convective flux rather than any change in protein permeability per se. The authors speculate that the increased microvascular permeability to water in vivo is mediated by direct interaction of glucose with the endothelial cells (perhaps with the glycocalyx).
Functional connections and pathways of coenzyme Q10‐inducible genes: An in‐silico study
Authors: Döring Frank , Schmelzer Constance , Lindner Inka , Vock Christina , Fujii Kenji 
Published: September 2007

AbstractCoenzyme Q10 (CoQ10, ubiquinone) is an essential cofactor in the electron transport chain, serves as a potent antioxidant in mitochondria and lipid membranes, and is often used as a dietary supplement for a number of diseases including cardiovascular diseases. Recently, we obtained evidence that CoQ10 (Kaneka Q10™) affects the expression of hundreds of human genes. To decipher the functional and regulatory connections of these genes, a literature search combined with transcription factor binding site analysis was performed using Genomatix BiblioSphere and MatInspector. This in‐silico analysis revealed 17 CoQ10‐inducible genes which are functionally connected by signalling pathways of G‐protein coupled receptors, JAK/STAT, integrin, and beta‐arrestin. Promoter analysis of these CoQ10‐inducible genes showed one group of NFκ B‐regulated genes, namely IL5, thrombin, vitronectin receptor and C‐reactive protein (CRP). Furthermore, a common promoter framework containing binding sites of the transcription factor families EVI1, HOXF, HOXC, and CLOX was identified in the promoters of IL5, CRP, and vitronectin receptor. The identified CoQ10‐inducible genes and pathways play an important role in inflammatory response. Since these effects are based on an in‐vitro study, the effect of CoQ10 on vascular health in vivo needs to be addressed in further animal and/or human intervention studies. IUBMB Life, 59: 628‐633, 2007
Implication of PKC in the seasonal variation of the immune response of the hemocytes of Mytilus galloprovincialis Lmk. and its role in interleukin‐2‐induced nitric oxide synthesis
Authors: Novas Ana , Barcia Ramiro , Ramos‐Martínez Juan Ignacio 
Published: September 2007

AbstractThe hemocytes are the cells responsible for the immune response in marine mollusks. The role of NO in processes related to the activation of the hemocytes has turned out evident over the late years. In the case of the mussel Mytilus galloprovincialis Lmk., hemocyte NO basal production varies throughout the year, showing a maximum in summer and a minimum in winter. IL‐2 reverts the low winter NO basal production through a process mediated by cAMP‐dependent protein kinase and by an apparent side effect of protein kinase C. The seasonal variation of NO production in the presence of the PKC inhibitor bisindolylmaleimide (BSM) allows suggesting a model in which PKC would modulate the activity of the enzymes responsible for nitric oxide production. IUBMB Life, 59: 659‐663, 2007
Identification of six new box C/D snoRNA gene clusters from rice
Authors: Li Wei , Jiang Ge , Zeng Dabo , Jin Youxin 
Published: September 2007

AbstractHere we have identified 18 different box C/D snoRNAs encoded in six new gene clusters by the screening of Oryza sativa (rice) genome sequences using a computer program that we have designed to search for non‐canonical box C and D sequences. Among this snoRNA collection, five are homologues of snoRNAs previously reported in other plants. One snoRNA is implicated to guide methylation at a corresponding site also modified in yeast rRNA but not in any other plants species yet examined. The other 12 snoRNAs are implicated in guiding 12 completely novel rRNA 2′‐O‐ribose methylation sites. We have verified the methylation of these rRNA sites by dNTP‐concentration dependent primer extension assay. The expression of all snoRNAs reported here was experimentally confirmed by primer extension assay. Polycistronic precursor transcripts from the gene clusters have been demonstrated by RT‐PCR. Thus it is highly likely that each of the rice snoRNA gene clusters identified here is transcribed in a polycistronic way, regardless of whether or not they are encoded within introns. This indicates that the mode of polycistronic expression of snoRNA clusters is widespread in rice, as is the case in Arabidopsis thaliana. IUBMB Life, 59: 664‐674, 2007
Sulfation of nitrotyrosine: Biochemistry and functional implications
Authors: Liu Ming‐Cheh , Yasuda Shin , Idell Steven 
Published: September 2007

AbstractNitration of tyrosine, in both protein‐bound form and free amino acid form, can readily occur in cells under oxidative/nitrative stress. In addition to serving as a biomarker of oxidative/nitrative stress, elevated levels of nitrotyrosine have been shown to cause DNA damage or trigger apoptosis. An important issue is whether the human body is equipped with mechanisms to counteract the potentially harmful effects of nitrotyrosine. Sulfate conjugation, as mediated by the cytosolic sulfotransferases (SULTs), is widely used for the biotransformation and disposal of a variety of drugs and other xenobiotics, as well as endogenous thyroid/steroid hormones and catecholamine neurotransmitters. Recent studies have revealed that the sulfation of nitrotyrosine occurs in cells under oxidative/nitrative stress, and have pinpointed the SULT1A3 as the responsible SULT enzyme. In this review, we summarized the available information concerning the biochemistry of nitrotyrosine sulfation and the effects of genetic polymorphisms on the nitrotyrosine sulfating activity of SULT1A3. Functional implications of the sulfation of nitrotyrosine are discussed. IUBMB Life, 622‐627, 2007
Comparative RNomics and Modomics in Mollicutes: Prediction of Gene Function and Evolutionary Implications
Authors: de Crécy‐Lagard Valérie , Marck Christian , Brochier‐Armanet Céline , Grosjean Henri 
Published: September 2007

AbstractStable RNAs are central to protein synthesis. Ribosomal RNAs make the core of the ribosome and provide the scaffold for accurate translation of mRNAs by a set of tRNA molecules each carrying an activated amino acid. To fulfill these important cellular functions, both rRNA and tRNA molecules require more than the four canonical bases and have recruited enzymes that introduce numerous modifications on nucleosides. Mollicutes are parasitic unicellular bacteria that originated from gram‐positive bacteria by considerably reducing their genome, reaching a minimal size of 480 kb in Mycoplasma genitalium. By analyzing the complete set of tRNA isoacceptors (tRNomics) and predicting the tRNA/rRNA modification enzymes (Modomics) among all sequenced Mollicutes (15 in all), our goal is to predict the minimal set of RNA modifications needed to sustain accurate translation of the cell's genetic information. Building on the known phylogenetic relationship of the 15 Mollicutes analyzed, we demonstrate that the solutions to reducing the RNA component of the translation apparatus vary from one Mollicute to the other and often rely on co‐evolution of specific tRNA isoacceptors and RNA modification enzymes. This analysis also reveals that only a few modification enzymes acting on nucleotides of the anticodon loop in tRNA (the wobble position 34 as well as in position 37, 3′‐adjacent to anticodon) and of the peptidyltransferase center of 23S rRNA appear to be absolutely essential and resistant to gene loss during the evolutionary process of genome reduction. IUBMB Life, 634‐658, 2007
Identification and biochemical properties of Dps (starvation‐induced DNA binding protein) from cyanobacterium Anabaena sp. PCC 7120
Authors: Wei Xiong , Mingjia He , Xiufeng Li , Yang Gao , Qingyu Wu 
Published: September 2007

AbstractDNA‐binding Proteins from Starved cells (Dps) are anti‐stress iron proteins preserving bacteria from oxidative damage. Based on sequence alignment, a 564‐bp open reading frame (all1173) encoding product in Anabaena sp. PCC 7120 shared high similarity with Dps family proteins. RT‐PCR showed all1173 is active at transcriptional level in Anabaena sp. PCC 7120 cells. We accordingly cloned the all1173 into prokaryotic expression system, purified the corresponding recombinant protein (Dps1173) and characterized its properties in vitro. According to CD spectrum and non‐denaturing electrophoresis assays, recombinant Dps1173 was alpha helix riched, and was likely to form dodecametric oligomer under native conditions. Fluorescence titration experiment revealed two major iron binding sites within Dps1173 monomer, indicating its potential ferroxidase activity. Although phenomena of direct DNA binding was not observed in Electrophoretic mobility shift assay, Dps1173 could also protect DNA from H2O2 stress for its iron scavenging capacity. This is the first description of Dps from heterocystous cyanobacterium Anabaena sp. PCC 7120. IUBMB Life, 59: 675‐681, 2007
Marsupial oocytes, fertilization and embryonic development can provide useful tools to study developmental mechanisms
Authors: Selwood Lynne 
Published: September 2007

AbstractAn analysis of several features of marsupial oocytes and developmental stages from the zygote to the neonate shows the advantages of studying these to answer questions about mammalian development in general. Marsupials make good model systems providing that species have well established breeding and husbandry protocols, a detailed time table of embryonic development associated with appropriate monitoring to collect desired stages and an induced ovulation protocol to allow collection of normal oocytes and developmental stages. One of the specific features of marsupial development that would provide further insight into problems in mammalian development is distinct oocyte and/or zygote polarity. Additionally, because the conceptus is transparent, cell‐cell associations can be studied until well after the hypoblast is formed. These combined features mean that lineage allocation and axis formation can be more easily studied and related to oocyte/zygote polarity and the order of cell division in these conceptuses. Another feature is the ability to collect normal unattached embryonic and fetal stages in some species and to culture conceptuses from the primitive streak stage to within a few hours of birth. This ability means that stages of organogenesis in most organ systems are readily accessible without the complications of implantation. IUBMB Life, 59: 617‐621, 2007
Developing a Virtual Library for 44,000 chemists
Authors: LEES Nigel 
Published: September 2007

ABSTRACTThis article describes how the Royal Society of Chemistry's library is making the transition from being a largely traditional print‐based library to one that offers remote‐access resources to its widespread membership. Key to its strategy is working with publishers and other content providers in a proactive and innovative way. Examples, case studies and difficulties faced are outlined alongside some of the solutions employed to facilitate the delivery of content.
Fighting plagiarism and IPR violation: why is it so important?
Authors: KULATHURAMAIYER Narayanan , MAURER Hermann 
Published: September 2007

ABSTRACTPlagiarism and intellectual property rights (IPR) violations have become a serious concern for many institutions and organizations. The revolutionary development of the Web presents numerous opportunities for such infringements to become even more widespread. This situation creates the risk of introducing a ‘culture of mediocrity'. This paper discusses these issues and proposes means of addressing the concerns by applying viable technological solutions.
Moving out of Oldenbourg's long shadow: what is the future for society publishing?
Authors: ARMBRUSTER Chris 
Published: September 2007

ABSTRACTThe Internet and the rise of e‐Science alter the conditions for scholarly communication. In signing declarations against open access mandates, society publishers indicate that they feel most threatened by the emergence of institutional repositories and the self‐archiving mandates that these make possible. More attention should be paid to the impact of e‐Science, the rise of Internet‐based guild publishers, and the entrance of players from the new economy. Society journals should stop aspiring to such functions as registration and archiving and should shed electronic dissemination, while enhancing certification and investing in (new) navigation services.
Open access developments in France: the HAL Open Archives System
Authors: BARUCH Pierre 
Published: September 2007

ABSTRACTThis article presents an overview of open access publishing and open access archiving in France. In natural sciences, most articles are published in international journals; authors must therefore comply with the policies of their publishers, irrespective of their nationality. For humanities and social sciences, where publication tends to be distributed among many small journals, portals have been created to provide electronic publishing, with varied access policies. Open archives repositories have been in existence in France since 2001; from 2006, a proactive policy led the main research agencies and universities to coordinate their actions towards a common archiving platform, HAL (Hyper Articles on Line), operated by CNRS (Centre National pour la Recherche Scientifique), with individual portals, either thematic or institutional. HAL stores now the majority of open access records – presently some 10–15% of French output – and is growing almost exponentially.
Launching an online‐only journal
Authors: STALKER Matt 
Published: September 2007

ABSTRACTIn May 2006, the Institution of Chemical Engineers (IChemE) launched its first exclusively online journal, Education for Chemical Engineers (http://www.icheme.org/ece). The author describes the editorial and marketing strategy behind the successful launch of the new title and the challenges facing a publisher when launching an ‘online‐only’ title. The article discusses how IChemE's established presence in the chemical engineering community benefited the new journal's launch and concludes with a list of key points to remember when launching a new product – with particular relevance to online titles.
Mapping the journal publishing landscape: how much do we know?
Authors: MORRIS Sally 
Published: September 2007

ABSTRACTIn debates about journals, their publishers and the future of both, it is important to be clear about what we are discussing. In this article, the sparse existing literature is surveyed, and original sources examined to provide further detail. The membership lists of six leading publishing associations, and the websites of their members, were also studied. More than half of all peer‐reviewed journals in Ulrich's are published by or on behalf of/in association with nonprofit organizations. Other than the top few commercial publishers, there is little difference in size between the two types; the ‘long tail’ of publishers are small and therefore vulnerable, and yet most are not represented by any trade association. The majority of journals come from the USA or the UK. Nonprofits launch fewer new journals, but are also less likely to close journals. The quality advantage of nonprofit journals may be reducing, but nonprofit journals still predominate among the most highly cited journals.
Fun&Co: identification of key functional differences in transcriptomes
Authors: Gamberoni Giacomo , Lamma Evelina , Lodo Gianluca , Marchesini Jlenia , Mascellani Nicoletta , Rossi Simona , Storari Sergio , Tagliavini Luca , Volinia Stefano 
Published: September 2007

AbstractMotivation: Microarray and other genome-wide technologies allow a global view of gene expression that can be used in several ways and whose potential has not been yet fully discovered. Functional insight into expression profiles is routinely obtained by using gene ontology terms associated to the cellular genes. In this article, we deal with functional data mining from expression profiles, proposing a novel approach that studies the correlations between genes and their relations to Gene Ontology (GO). We implemented this approach in a public web-based application named Fun&Co. By using Fun&Co, the user dissects in a pair-wise manner gene expression patterns and links correlated pairs to gene ontology terms. The proof of principle for our study was accomplished by dissecting molecular pathways in muscles. In particular, we identified specific cellular pathways by comparing the three different types of muscle in a pairwise fashion. In fact, we were interested in the specific molecular mechanisms regulating the cardiovascular system (cardiomyocytes and smooth muscle cells).Results: We applied here Fun&Co to the molecular study of cardiovascular system and the identification of the specific molecular pathways in heart, skeletal and smooth muscles (using 317 microarrays) and to reveal functional differences between the three different kinds of muscle cells.Availability: Application is online at http://tommy.unife.it.Contact: s.volinia@unife.itSupplementary information: Supplementary data are available at Bioinformatics online.
TreeSnatcher: coding trees from images
Authors: Laubach Thomas , von Haeseler Arndt 
Published: September 2007

Abstract
Summary: TreeSnatcher is a GUI-driven JAVA application for the semi-automatic recognition of multifurcating phylogenetic trees in pixel images. The program accepts an image file as input and analyzes the topology and the metrics of a tree depicted. The analysis is carried out in a multiple-stage process using algorithms from image analysis. In the end, TreeSnatcher produces a Newick tree code that represents the tree structure optionally including branch lengths. TreeSnatcher can process trees with 100 leaves or more in a few seconds.
Availability: TreeSnatcher was developed in JAVA under Mac OS X and is executable on UNIX/Linux, Windows and Mac OS X systems. The application and its documentation can be freely downloaded from http://www.cibiv.at/software/treesnatcher.
Contact: arndt.von.haeseler@univie.ac.at
The high-level similarity of some disparate gene expression measures
Authors: Raghavan Nandini , De Bondt An M. I. M. , Talloen Willem , Moechars Dieder , Göhlmann Hinrich W. H. , Amaratunga Dhammika 
Published: September 2007

AbstractProbe-level data from Affymetrix GeneChips can be summarized in many ways to produce probe-set level gene expression measures (GEMs). Disturbingly, the different approaches not only generate quite different measures but they could also yield very different analysis results. Here, we explore the question of how much the analysis results really do differ, first at the gene level, then at the biological process level. We demonstrate that, even though the gene level results may not necessarily match each other particularly well, as long as there is reasonably strong differentiation between the groups in the data, the various GEMs do in fact produce results that are similar to one another at the biological process level. Not only that the results are biologically relevant. As the extent of differentiation drops, the degree of concurrence weakens, although the biological relevance of findings at the biological process level may yet remain.Contact: damaratu@prdus.jnj.comSupplementary information: Supplementary data are available at Bioinformatics online.
Idiographica: a general-purpose web application to build idiograms on-demand for human, mouse and rat
Authors: Kin Taishin , Ono Yukiteru 
Published: September 2007

AbstractSummary: We have launched a web server, which serves as a general-purpose idiogram rendering service, and allows users to generate high-quality idiograms with custom annotation according to their own genome-wide mapping/annotation data through an easy-to-use interface. The generated idiograms are suitable not only for visualizing summaries of genome-wide analysis but also for many types of presentation material including web pages, conference posters, oral presentations, etc.Availability: Idiographica is freely available at http://www.ncrna.org/idiographica/Contact: kin-taishin@aist.go.jp
Inferring transcriptional regulatory networks from high-throughput data
Authors: Wang Rui-Sheng , Wang Yong , Zhang Xiang-Sun , Chen Luonan 
Published: September 2007

AbstractMotivation: Inferring the relationships between transcription factors (TFs) and their targets has utmost importance for understanding the complex regulatory mechanisms in cellular systems. However, the transcription factor activities (TFAs) cannot be measured directly by standard microarray experiment owing to various post-translational modifications. In particular, cooperative mechanism and combinatorial control are common in gene regulation, e.g. TFs usually recruit other proteins cooperatively to facilitate transcriptional reaction processes.Results: In this article, we propose a novel method for inferring transcriptional regulatory networks (TRN) from gene expression data based on protein transcription complexes and mass action law. With gene expression data and TFAs estimated from transcription complex information, the inference of TRN is formulated as a linear programming (LP) problem which has a globally optimal solution in terms of L1 norm error. The proposed method not only can easily incorporate ChIP-Chip data as prior knowledge, but also can integrate multiple gene expression datasets from different experiments simultaneously. A unique feature of our method is to take into account protein cooperation in transcription process. We tested our method by using both synthetic data and several experimental datasets in yeast. The extensive results illustrate the effectiveness of the proposed method for predicting transcription regulatory relationships between TFs with co-regulators and target genes.Availability: The software TRNinfer is available from http://intelligent.eic.osaka-sandai.ac.jp/chenen/TRNinfer.htmContact: chen@eic.osaka-sandai.ac.jp and zxs@amt.ac.cnSupplementry information: Supplementary data are available at Bioinformatics online.