bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does Improved Detection of Blunt Vertebral Artery Injuries Lead to Improved Outcomes? Analysis of the National Trauma Data Bank®
Authors: Spaniolas Konstantinos , Velmahos George C. , Alam Hasan B. , de Moya Marc , Tabbara Malek , Sailhamer Elizabeth 
Published: July 2008

AbstractBackgroundThe rate of blunt vertebral artery (BVI) has increased in institutions using aggressive screening protocols. It is unclear whether earlier diagnosis and therapy have improved outcomes. Our goal was to estimate the national incidence of BVI and BVI‐related stroke (BVI‐S), and report on the functional outcome of patients with this diagnosis.MethodsThe annual rates of BVI and BVI‐S were estimated by using the National Trauma Data Bank (NTDB®) from 2001 to 2005. The functional outcome was evaluated by the modified functional independence measure (FIM) score (range, 3–12).ResultsA total of 574 patients with BVI were identified among the 761,385 blunt trauma admissions (0.075% overall incidence). BVI‐S was diagnosed in 12% of patients with BVI and no associated blunt carotid injury. The FIM on discharge was 9.62 ± 2.78 (range, 3–12), and 49% of the patients showed complete functional independence. Overall mortality was 8%. The annual incidence showed a steady increase from 0.053% in 2001 to 0.1% in 2005 (p < 0.001). No difference in annual BVI‐S and complete functional independence was observed.ConclusionsAs a result of increased awareness, the nation‐wide rate of detection of BVI has doubled in recent years. However, BVI‐S rates and functional outcome have not improved, raising questions about the available treatment protocols.
Helicobacter pylori‐Induced Damage to the Gastric Mucosa is Not Modulated by Previous Vagotomy or Medical Treatment of Peptic Ulcer Disease: A Comparative Study of Vagotomized Patients, Medically Treated Peptic Ulcer Patients and Community Control Subjects
Authors: Lindsetmo Rolv‐Ole , Eide Tor Jac , Johnsen Roar , Revhaug Arthur 
Published: July 2008

AbstractBackgroundAn increase in the prevalence of precancerous lesions and atrophic changes in the gastric mucosa has been reported as long‐term consequences of vagotomy‐induced acid suppression. This study was designed to describe the long‐term changes in the gastric mucosa caused by vagotomy and Helicobacter pylori infection.MethodsSeventy‐nine patients with vagotomized peptic ulcers, 70 nonoperated patients with peptic ulcers, and 85 matched community control subjects were randomly selected to participate in an upper endoscopic study. Biopsy specimens were taken from predestined locations of the gastric mucosa.ResultsMean follow‐up time for the vagotomized patients was 17.3 (range, 6–28) years and 12.7 (range, 10–17) years for the medically treated peptic ulcer patients. In H. pylori‐positive subjects, severe atrophic changes in the distal gastric mucosa (prepylorus and angulus) was found in 30% (95% confidence interval (CI), 19–43) of the vagotomized patients and in 43% (95% CI, 29–58) of medically treated patients with peptic ulcers, and in 32% (95% CI, 20–46) of the community control subjects. Severe intestinal metaplasia was not found more frequently in vagotomized peptic ulcer patients compared with medically treated patients with peptic ulcers (p = 0.5). The histological picture of the age‐matched community control subjects did not differ significantly from the patients with peptic ulcers when corrected for presence of H. pylori infection.ConclusionsThis study lends no support to theories of increased premalignant changes in the gastric mucosa of vagotomized patients. H. pylori infection rather than long‐term acid suppression seems to be the explanation of the gastric mucosal changes seen after vagotomy.
Functional role of periostin in development and wound repair: implications for connective tissue disease
Authors: Hamilton Douglas W. 
Published: July 2008

AbstractIntegrity of the extracellular matrix (ECM) is essential for maintaining the normal structure and function of connective tissues. ECM is secreted locally by cells and organized into a complex meshwork providing physical support to cells, tissues, and organs. Initially thought to act only as a scaffold, the ECM is now known to provide a myriad of signals to cells regulating all aspects of their phenotype from morphology to differentiation. Matricellular proteins are a class of ECM related molecules defined through their ability to modulate cell–matrix interactions. Matricellular proteins are expressed at high levels during development, but typically only appear in postnatal tissue in wound repair or disease, where their levels increase substantially. Members of the CCN family, tenascin‐C, osteopontin, secreted protein acidic rich in cysteine (SPARC), bone sialoprotein, thrombospondins, and galectins have all been classed as matricellular proteins. Periostin, a 90 kDa secreted homophilic cell adhesion protein, was recently added to matricellular class of proteins based on its expression pattern and function during development as well as in wound repair. Periostin is expressed in connective tissues including the periodontal ligament, tendons, skin and bone, and is also prominent in neoplastic tissues, cardiovascular disease, as well as in connective tissue wound repair. This review will focus on the functional role of periostin in tissue physiology. Fundamentally, it appears that periostin influences cell behaviour as well as collagen fibrillogenesis, and therefore exerts control over the structural and functional properties of connective tissues in both health and disease. Periostin is a novel matricellular protein with close homology to Drosophila fasciclin 1. In this review, the functional role of periostin is discussed in the context of connective tissue physiology, in development, disease, and wound repair.
Pharmacological properties of purinergic receptors and their effects on proliferation and induction of neuronal differentiation of P19 embryonal carcinoma cells
Authors: Resende R.R. , Britto L.R.G. , Ulrich H. 
Published: July 2008

AbstractWe have used P19 embryonal carcinoma cells asin vitromodel for early neurogenesis to study ionotropic P2X and metabotropic P2Y receptor‐induced Ca2+transients and their participation in induction of proliferation and differentiation. In embryonic P19 cells, P2Y1, P2Y2and P2X4receptors or P2X‐heteromultimers with similar P2X4pharmacology were responsible for ATP and ATP analogue‐induced Ca2+transients. In neuronal‐differentiated cells, P2Y2,P2Y6, P2X2and possibly P2X2/P2X6heteromeric receptors were the major mediators of the elevations in intracellular free calcium concentration [Ca2+]i. We have collected evidence for the involvement of metabotropic purinergic receptors in proliferation induction of undifferentiated and neural progenitor cells by using a BrdU‐incorporation assay. ATP‐, UTP‐, ADP‐, 2‐MeS‐ATP‐ and ADP‐βS‐induced proliferation in P19 cells was mediated by P2Y1and P2Y2receptors as judged from pharmacological profiles of receptor responses. ATP‐provoked acceleration of neuronal differentiation, determined by analysis of nestin and neuron‐specific enolase gene and protein expression, also resulted from P2Y1and P2Y2receptor activation. Proliferation‐ and differentiation‐induction involved the activation of inositol‐trisphosphate sensitive intracellular Ca2+stores.
SOME WEAKER FORMS OF THE CHAIN (F) CONDITION FOR METACOMPACTNESS
Authors: VURAL ÇETIN 
Published: July 2008

AbstractWe define, in a slightly unusual way, the rank of a partially ordered set. Then we prove that if X is a topological space and $\mathcal {W}=\{\mathcal {W}(x):x \in X\}$ satisfies condition (F) and, for every x∈X, $\mathcal {W}(x)$ is of the form $\bigcup _{i \in n(x)}\mathcal {W}_{i}(x)$, where $\mathcal {W}_{0}(x)$ is Noetherian of finite rank, and every other $\mathcal {W}_{i}(x)$ is a chain (with respect to inclusion) of neighbourhoods of x, then X is metacompact. We also obtain a cardinal extension of the above. In addition, we give a new proof of the theorem ‘if the space X has a base $\mathcal {B}$ of point-finite rank, then X is metacompact’, which was proved by Gruenhage and Nyikos.
Conditional knockout of nucleolin in DT40 cells reveals the functional redundancy of its RNA‐binding domains
Authors: Storck Sébastien , Thiry Marc , Bouvet Philippe 
Published: July 2008

Background information. Nucleolin is a major nucleolar protein which is highly expressed in rapidly dividing cells and cancer cell lines. This protein is claimed to be multifunctional and could play a role in rRNA (ribosomal RNA) synthesis, as well as in cell division or response to cellular stresses. Therefore, how nucleolin influences cell proliferation remained elusive so far.Results. We have generated conditional nucleolin‐knockout cells using the chicken B lymphocyte cell line DT40. Our results indicate that nucleolin is absolutely required for the proliferation and for the survival of these cells. Depletion of nucleolin drastically inhibits rDNA (ribosomal DNA) transcription while only slightly affecting pre‐rRNA processing. This inhibition is accompanied by modifications of the shape and the structure of the nucleolus. The analysis of mutants of nucleolin, which lack two or three RNA‐binding domains, shows that these domains harbour redundant functions and that nucleolin's roles in transcription, rRNA maturation and nucleolar shape can be partially uncoupled.Conclusions. The function of nucleolin in ribosomal synthesis could account for its effect on cell division and survival, but this vital role does not seem to be linked to sequence‐specific RNA binding.
Message-passing algorithms for the prediction of protein domain interactions from protein–protein interaction data
Authors: Iqbal Mudassar , Freitas Alex A. , Johnson Colin G. , Vergassola Massimo 
Published: July 2008

Abstract
Motivation: Cellular processes often hinge upon specific interactions among proteins, and knowledge of these processes at a system level constitutes a major goal of proteomics. In particular, a greater understanding of protein–protein interactions can be gained via a more detailed investigation of the protein domain interactions that mediate the interactions of proteins. Existing high-throughput experimental techniques assay protein–protein interactions, yet they do not provide any direct information on the interactions among domains. Inferences concerning the latter can be made by analysis of the domain composition of a set of proteins and their interaction map. This inference problem is non-trivial, however, due to the high level of noise generally present in experimental data concerning protein–protein interactions. This noise leads to contradictions, i.e. the impossibility of having a pattern of domain interactions compatible with the protein–protein interaction map.
Results: We formulate the problem of prediction of protein domain interactions in a form that lends itself to the application of belief propagation, a powerful algorithm for such inference problems, which is based on message passing. The input to our algorithm is an interaction map among a set of proteins, and a set of domain assignments to the relevant proteins. The output is a list of probabilities of interaction between each pair of domains. Our method is able to effectively cope with errors in the protein–protein interaction dataset and systematically resolve contradictions. We applied the method to a dataset concerning the budding yeast Saccharomyces cerevisiae and tested the quality of our predictions by cross-validation on this dataset, by comparison with existing computational predictions, and finally with experimentally available domain interactions. Results compare favourably to those by existing algorithms.
Availability: A C language implementation of the algorithm is available upon request.
Contact: mi26@kent.ac.uk
The use of meiofauna diversity as an indicator of pollution in harbours
Authors: Moreno Mariapaola , Vezzulli Luigi , Marin Valentina , Laconi Paola , Albertelli Giancarlo , Fabiano Mauro 
Published: July 2008

Abstract
Moreno, M., Vezzulli, L., Marin, V., Laconi, P., Albertelli, G., and Fabiano, M. 2008. The use of meiofauna diversity as an indicator of pollution in harbours. – ICES Journal of Marine Science, 65: 1428–1435. We assessed several meiofaunal indices in sediments of three Mediterranean harbours differing in environmental contamination to evaluate their usefulness as indicators of pollution and to identify those that best described environmental quality. In general, indicators based on meiofaunal taxa demonstrated a significant correlation with the concentration of contaminants, especially the polycyclic aromatic hydrocarbons (PAHs). Nematode genus-based indicators correlated with contaminant concentrations at similar levels of significance, suggesting that a high taxonomic resolution does not improve the information content of meiofauna diversity indicators for assessing the environmental quality in these harbours. Notably, environmental variables that affect meiofaunal and nematode assemblages (e.g. water depth, grain size, and food sources) demonstrated a low spatial and temporal variability in the harbours investigated and did not represent important confounding factors. We conclude that the application of meiofaunal and nematode indices can be a useful tool for assessing the environmental quality of harbour ecosystems.
Phenotypic engineering by reprogramming gene transcription using novel artificial transcription factors in Escherichia coli
Authors: Lee Ju Young , Sung Bong Hyun , Yu Byung Jo , Lee Jun Hyoung , Lee Sang Hee , Kim Mi Sun , Koob Michael D. , Kim Sun Chang 
Published: July 2008

Abstract
Now that many genomes have been sequenced and the products of newly identified genes have been annotated, the next goal is to engineer the desired phenotypes in organisms of interest. For the phenotypic engineering of microorganisms, we have developed novel artificial transcription factors (ATFs) capable of reprogramming innate gene expression circuits in Escherichia coli. These ATFs are composed of zinc finger (ZF) DNA-binding proteins, with distinct specificities, fused to an E. coli cyclic AMP receptor protein (CRP). By randomly assembling 40 different types of ZFs, we have constructed more than 6.4 × 104 ATFs that consist of 3 ZF DNA-binding domains and a CRP effector domain. Using these ATFs, we induced various phenotypic changes in E. coli and selected for industrially important traits, such as resistance to heat shock, osmotic pressure and cold shock. Genes associated with the heat-shock resistance phenotype were then characterized. These results and the general applicability of this platform clearly indicate that novel ATFs are powerful tools for the phenotypic engineering of microorganisms and can facilitate microbial functional genomic studies.
Computational Comparison of Human Genomic Sequence Assemblies for a Region of Chromosome 4
Authors: Semple Colin A.M. , Morris Stewart W. , Porteous David J. , Evans Kathryn L. 
Published: July 2008

Much of the available human genomic sequence data exist in a fragmentary draft state following the completion of the initial high-volume sequencing performed by the International Human Genome Sequencing Consortium (IHGSC) and Celera Genomics (CG). We compared six draft genome assemblies over a region of chromosome 4p (D4S394–D4S403), two consecutive releases by the IHGSC at University of California, Santa Cruz (UCSC), two consecutive releases from the National Centre for Biotechnology Information (NCBI), the public release from CG, and a hybrid assembly we have produced using IHGSC and CG sequence data. This region presents particular problems for genomic sequence assembly algorithms as it contains a large tandem repeat and is sparsely covered by draft sequences. The six assemblies differed both in terms of their relative coverage of sequence data from the region and in their estimated rates of misassembly. The CG assembly method attained the lowest level of misassembly, whereas NCBI and UCSC assemblies had the highest levels of coverage. All assemblies examined included <60% of the publicly available sequence from the region. At least 6% of the sequence data within the CG assembly for the D4S394–D4S403 region was not present in publicly available sequence data. We also show that even in a problematic region, existing software tools can be used with high-quality mapping data to produce genomic sequence contigs with a low rate of rearrangements.[All sequence accessions for the genomic sequence assemblies analyzed and the data sets used to assess coverage and rates of misassembly are available from http://www.ed.ac.uk/∼csemple.]
Combining Mouse Congenic Strains and Microarray Gene Expression Analyses to Study a Complex Trait: The NOD Model of Type 1 Diabetes
Authors: Eaves Iain A. , Wicker Linda S. , Ghandour Ghassan , Lyons Paul A. , Peterson Laurence B. , Todd John A. , Glynne Richard J. 
Published: July 2008

Combining congenic mapping with microarray expression profiling offers an opportunity to establish functional links between genotype and phenotype for complex traits such as type 1 diabetes (T1D). We used high-density oligonucleotide arrays to measure the relative expression levels of >39,000 genes and ESTs in the NOD mouse (a murine model of T1D and other autoimmune conditions), four NOD-derived diabetes-resistant congenic strains, and two nondiabetic control strains. We developed a simple, yet general, method for measuring differential expression that provides an objective assessment of significance and used it to identify >400 gene expression differences and eight new candidates for theIdd9.1locus. We also discovered a potential early biomarker for autoimmune hemolytic anemia that is based on different levels of erythrocyte-specific transcripts in the spleen. Overall, however, our results suggest that the dramatic disease protection conferred by sixIddloci (Idd3,Idd5.1, Idd5.2, Idd9.1, Idd9.2, andIdd9.3) cannot be rationalized in terms of global effects on the noninduced immune system. They also illustrate the degree to which regulatory systems appear to be robust to genetic variation. These observations have important implications for the design of future microarray-based studies in T1D and, more generally, for studies that aim to combine genome-wide expression profiling and congenic mapping.[The supplemental research data accompanying this article are available through the authors' web site (http://www-gene.cimr.cam.ac.uk/todd/), and the array data have been submitted to the GEO data repository (http://www.ncbi.nlm.nih.gov/geo/) under accession no. GSE11]
Novel Fluorescence Labeling and High-Throughput Assay Technologies for In Vitro Analysis of Protein Interactions
Authors: Doi Nobuhide , Takashima Hideaki , Kinjo Masataka , Sakata Kyoko , Kawahashi Yuko , Oishi Yuko , Oyama Rieko , Miyamoto-Sato Etsuko , Sawasaki Tatsuya , Endo Yaeta , Yanagawa Hiroshi 
Published: July 2008

We developed and tested a simple method for fluorescence labeling and interaction analysis of proteins based on a highly efficient in vitro translation system combined with high-throughput technologies such as microarrays and fluorescence cross-correlation spectroscopy (FCCS). By use of puromycin analogs linked to various fluorophores through a deoxycytidylic acid linker, a single fluorophore can be efficiently incorporated into a protein at the carboxyl terminus during in vitro translation. We confirmed that the resulting fluorescently labeled proteins are useful for probing protein–protein and protein–DNA interactions by means of pulldown assay, DNA microarrays, and FCCS in model experiments. These fluorescence assay systems can be easily extended to highly parallel analysis of protein interactions in studies of functional genomics.[Online supplementary material available at http://www.genome.org.]
GFScan: A Gene Family Search Tool at Genomic DNA Level
Authors: Xuan Zhenyu , McCombie W. Richard , Zhang Michael Q. 
Published: July 2008

We have developed GFScan (GeneFamily Scan), a tool that identifies members of a gene family by searching genomic DNA sequences with genomic DNA motifs (or matrices) that are representative of the family. We have tested GFScan on four human gene families including the neurotransmitter-gated ion-channels (NGIC) family, the carbonic anhydrases (CA) family, the Dbl homology (DH) domain family, and the ETS-domain family. All known members of these families with motifs mapped to sequenced genomic DNA regions were found, whereas some novel genomic locations were also found to match the motifs, which may indicate new members in these families. Compared with other methods,GFScan recognized all true positives with much fewer false positives. We also showed that motifs constructed based on human genes could be used to search the mouse genome to identify orthologous family members in mouse. This program is available athttp://www.cshl.org/mzhanglab/.[The following individuals and institutions kindly provided reagents, samples or unpublished information as indicated in the paper: J. Maddock and Celera Genomics.]
Analyses of the Extent of Shared Synteny and Conserved Gene Orders between the Genome of Fugu rubripes and Human 20q
Authors: Smith Sarah F. , Snell Philip , Gruetzner Frank , Bench Anthony J. , Haaf Thomas , Metcalfe Judith A. , Green Anthony R. , Elgar Greg 
Published: July 2008

Cosmid and BAC contig maps have been constructed across twoFugu genomic regions containing the orthologs of human genes mapping to human chromosome 20q. Contig gene contents have been assessed by sample sequencing and comparative database analyses. Contigs are centered around two Fugu topoisomerase1 (top1) genes that were initially identified by sequence similarity to humanTOP1 (20q12). Two other genes (SNAI1 andKRML) mapping to human chromosome 20 are also duplicated inFugu. The two contigs have been mapped to separateFugu chromosomes. Our data indicate that these linkage groups result from the duplication of an ancestral chromosome segment containing at least 40 genes that now map to the long arm of human chromosome 20. Although there is considerable conservation of synteny, gene orders are not well conserved between Fugu and human, with only very short sections of two to three adjacent genes being maintained in both organisms. Comparative analyses have allowed this duplication event to be dated before the separation of Fuguand zebrafish. Our data (which are best explained by regional duplication, followed by substantial gene loss) support the hypothesis that there have been a large number of gene and regional duplications (and corresponding gene loss) in the fish lineage, possibly resulting from a single whole genome duplication event.[Reagents, samples, and unpublished information freely provided by D. Barnes and I.D. Hickson.]