bluuebunny/crossref_metadata_2025_split huggingface dataset:
Possible Misidentification of Rain Type by TRMM PR over Tibetan Plateau
Authors: Fu Yunfei , Liu Guosheng 
Published: May 2007

AbstractRain-type statistics derived from Tropical Rainfall Measuring Mission (TRMM) precipitation radar (PR) standard product show that some 70% of raining pixels in the central Tibetan Plateau summer are stratiform—a clear contradiction to the common knowledge that rain events during summer in this region are mostly convective, as a result of the strong atmospheric convective instability resulting from surface heating. In examining the vertical distribution of the stratiform rain-rate profiles, it is suspected that the TRMM PR algorithm misidentifies weak convective rain events as stratiform rain events. The possible cause for this misidentification is believed to be that the freezing level is close to the surface over the plateau, so that the ground echo may be mistakenly identified as the melting level in the PR rain classification algorithm.
A survey of 14 to 16 year olds as to their attitude toward and use of sunbeds
Authors: Mackay H. , Lowe D. , Edwards D. , Rogers S.N. 
Published: May 2007

Objective Sunbeds pose a potential risk to health. Although not recommended for children under 16 years of age they are used by this age group. The purpose of this study was to assess the awareness of suntanning guidelines, the use of sunbeds and the attitude towards tanning in children aged between 14 and 16 years. Design and method 499 pupils aged 14 to 16 years responded to a questionnaire survey in two schools in a mixed urban part of Merseyside. Results Overall, sunbeds had been used by 43 per cent of pupils. Girls had used them much more than boys with use increasing by age for both sexes. Overall, 65 per cent said they were aware of guidelines. About half thought that guidelines advising people how often to use a sunbed were a good thing. One in 10 of those using a sunbed also said they had had problems with their eyes or skin. Most boy and girl users thought using sunbeds made them look healthy, made them more attractive and confident, that they created a base tan before a holiday and that they were a good treatment for spots. Conclusion There is considerable awareness of sunbed guidelines; however, sunbed use in the under 16 year age group remains high. This poses a public health issue and better education and enforcement strategies are required.
High T-cell response to human cytomegalovirus induces chemokine-mediated endothelial cell damage
Authors: Bolovan-Fritts Cynthia A. , Trout Rodney N. , Spector Stephen A. 
Published: May 2007

Abstract
Human cytomegalovirus (CMV) infection has been linked to inflammatory diseases that involve vascular endothelial damage, including vascular disease and chronic transplant rejection. We previously reported that the host CD4+ T-cell response to CMV antigen presented by endothelial cells can produce interferon-γ and tumor necrosis factor-α at levels sufficient to drive induction of fractalkine, a key marker of inflammation, in endothelial cells. In this work, we report that donors with high frequencies of antigen-specific T cells to CMV (high responders) induce higher levels of activation-associated chemokines such as fractalkine, RANTES (regulated on activation, normal T cell expressed and secreted), and macrophage inflammatory protein-1β, together with cell-adhesion markers in endothelial cells compared with donors with low levels of CMV-specific T cells (low responders). High-responder cultures had higher levels of leukocyte recruitment and adherence to the endothelial monolayers associated with progressive damage and loss of the endothelial cells. These processes that led to endothelial destruction only required viral antigen and did not require infectious virus. Our findings further support that CMV may represent one member of a class of persistent pathogens in which a high antigen-specific T-cell response defines an important risk factor for development of chronic inflammation and endothelial cell injury.
Robust detection and verification of linear relationships to generate metabolic networks using estimates of technical errors
Authors: Kose Frank , Budczies Jan , Holschneider Matthias , Fiehn Oliver 
Published: May 2007

Abstract

Background
The size and magnitude of the metabolome, the ratio between individual metabolites and the response of metabolic networks is controlled by multiple cellular factors. A tight control over metabolite ratios will be reflected by a linear relationship of pairs of metabolite due to the flexibility of metabolic pathways. Hence, unbiased detection and validation of linear metabolic variance can be interpreted in terms of biological control. For robust analyses, criteria for rejecting or accepting linearities need to be developed despite technical measurement errors. The entirety of all pair wise linear metabolic relationships then yields insights into the network of cellular regulation.

Results
The Bayesian law was applied for detecting linearities that are validated by explaining the residues by the degree of technical measurement errors. Test statistics were developed and the algorithm was tested on simulated data using 3–150 samples and 0–100% technical error. Under the null hypothesis of the existence of a linear relationship, type I errors remained below 5% for data sets consisting of more than four samples, whereas the type II error rate quickly raised with increasing technical errors. Conversely, a filter was developed to balance the error rates in the opposite direction. A minimum of 20 biological replicates is recommended if technical errors remain below 20% relative standard deviation and if thresholds for false error rates are acceptable at less than 5%. The algorithm was proven to be robust against outliers, unlike Pearson's correlations.

Conclusion
The algorithm facilitates finding linear relationships in complex datasets, which is radically different from estimating linearity parameters from given linear relationships. Without filter, it provides high sensitivity and fair specificity. If the filter is activated, high specificity but only fair sensitivity is yielded. Total error rates are more favorable with deactivated filters, and hence, metabolomic networks should be generated without the filter. In addition, Bayesian likelihoods facilitate the detection of multiple linear dependencies between two variables. This property of the algorithm enables its use as a discovery tool and to generate novel hypotheses of the existence of otherwise hidden biological factors.
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
Authors: Grissa Ibtissem , Vergnaud Gilles , Pourcel Christine 
Published: May 2007

Abstract

Background
In Archeae and Bacteria, the repeated elements called CRISPRs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. Short sequences called spacers are stored in-between repeated elements. In the current model, motifs comprising spacers and repeats may target an invading DNA and lead to its degradation through a proposed mechanism similar to RNA interference. Analysis of intra-species polymorphism shows that new motifs (one spacer and one repeated element) are added in a polarised fashion. Although their principal characteristics have been described, a lot remains to be discovered on the way CRISPRs are created and evolve. As new genome sequences become available it appears necessary to develop automated scanning tools to make available CRISPRs related information and to facilitate additional investigations.

Description
We have produced a program, CRISPRFinder, which identifies CRISPRs and extracts the repeated and unique sequences. Using this software, a database is constructed which is automatically updated monthly from newly released genome sequences. Additional tools were created to allow the alignment of flanking sequences in search for similarities between different loci and to build dictionaries of unique sequences. To date, almost six hundred CRISPRs have been identified in 475 published genomes. Two Archeae out of thirty-seven and about half of Bacteria do not possess a CRISPR. Fine analysis of repeated sequences strongly supports the current view that new motifs are added at one end of the CRISPR adjacent to the putative promoter.

Conclusion
It is hoped that availability of a public database, regularly updated and which can be queried on the web will help in further dissecting and understanding CRISPR structure and flanking sequences evolution. Subsequent analyses of the intra-species CRISPR polymorphism will be facilitated by CRISPRFinder and the dictionary creator. CRISPRdb is accessible at http://crispr.u-psud.fr/crispr
Clustering protein environments for function prediction: finding PROSITE motifs in 3D
Authors: Yoon Sungroh , Ebert Jessica C , Chung Eui-Young , De Micheli Giovanni , Altman Russ B 
Published: May 2007

Abstract

Background
Structural genomics initiatives are producing increasing numbers of three-dimensional (3D) structures for which there is little functional information. Structure-based annotation of molecular function is therefore becoming critical. We previously presented FEATURE, a method for describing microenvironments around functional sites in proteins. However, FEATURE uses supervised machine learning and so is limited to building models for sites of known importance and location. We hypothesized that there are a large number of sites in proteins that are associated with function that have not yet been recognized. Toward that end, we have developed a method for clustering protein microenvironments in order to evaluate the potential for discovering novel sites that have not been previously identified.

Results
We have prototyped a computational method for rapid clustering of millions of microenvironments in order to discover residues whose surrounding environments are similar and which may therefore share a functional or structural role. We clustered nearly 2,000,000 environments from 9,600 protein chains and defined 4,550 clusters. As a preliminary validation, we asked whether known 3D environments associated with PROSITE motifs were "rediscovered". We found examples of clusters highly enriched for residues that share PROSITE sequence motifs.

Conclusion
Our results demonstrate that we can cluster protein environments successfully using a simplified representation and K-means clustering algorithm. The rediscovery of known 3D motifs allows us to calibrate the size and intercluster distances that characterize useful clusters. This information will then allow us to find new clusters with similar characteristics that represent novel structural or functional sites.
Using indirect protein interactions for the prediction of Gene Ontology functions
Authors: Chua Hon Nian , Sung Wing-Kin , Wong Limsoon 
Published: May 2007

AbstractBackgroundProtein-protein interaction has been used to complement traditional sequence homology to elucidate protein function. Most existing approaches only make use of direct interactions to infer function, and some have studied the application of indirect interactions for functional inference but are unable to improve prediction performance. We have previously proposed an approach, FS-Weighted Averaging, which uses topological weighting and level-2 indirect interactions (protein pairs connected via two interactions) for predicting protein function from protein interactions and have found that it yields predictions with superior precision on yeast proteins over existing approaches. Here we study the use of this technique to predict functional annotations from the Gene Ontology for seven genomes:Saccharomyces cerevisiae,Drosophila melanogaster,Caenorhabditis elegans,Arabidopsis thaliana,Rattus norvegicus,Mus musculus, andHomo sapiens.ResultsOur analysis shows that protein-protein interactions provide supplementary coverage over sequence homology in the inference of protein function and is definitely a complement to sequence homology. We also find that FS-Weighted Averaging consistently outperforms two classical approaches, Neighbor Counting and Chi-Square, across the seven genomes for all three categories of the Gene Ontology. By randomly adding and removing interactions from the interactions, we find that Weighted Averaging is also rather robust against noisy interaction data.ConclusionWe have conducted a comprehensive study over seven genomes. We conclude that FS-Weighted Averaging can effectively make use of indirect interactions to make the inference of protein functions from protein interactions more effective. Furthermore, the technique is general enough to work over a variety of genomes.
The chemokine Sdf-1 and its receptor Cxcr4 are required for formation of muscle in zebrafish
Authors: Chong Shang-Wei , Nguyet Le-Minh , Jiang Yun-Jin , Korzh Vladimir 
Published: May 2007

AbstractBackgroundDuring development cell migration takes place prior to differentiation of many cell types. The chemokine receptor Cxcr4 and its ligand Sdf1 are implicated in migration of several cell lineages, including appendicular muscles.ResultsWe dissected the role ofsdf1-cxcr4during skeletal myogenesis. We demonstrated that the receptorcxcr4ais expressed in the medial-anterior part of somites, suggesting that chemokine signaling plays a role in this region of the somite. Previous reports emphasized co-operation of Sdf1a and Cxcr4b. We found that during early myogenesis Sdf1a co-operates with the second Cxcr4 of zebrafish – Cxcr4a resulting in the commitment of myoblast to form fast muscle. Disrupting this chemokine signal caused a reduction inmyoDandmyf5expression and fast fiber formation. In addition, we showed that a dimerization partner of MyoD and Myf5, E12, positively regulates transcription ofcxcr4aandsdf1ain contrast to that of Sonic hedgehog, which inhibited these genes through induction of expression ofid2.ConclusionWe revealed a regulatory feedback mechanism betweencxcr4a-sdf1aand genes encoding myogenic regulatory factors, which is involved in differentiation of fast myofibers. This demonstrated a role of chemokine signaling during development of skeletal muscles.
The promoter and transcribed regions of the Leishmania tarentolae spliced leader RNA gene array are devoid of nucleosomes
Authors: Hitchcock Robert A , Thomas Sean , Campbell David A , Sturm Nancy R 
Published: May 2007

Abstract

Background
The spliced leader (SL) RNA provides the 5' m7G cap and first 39 nt for all nuclear mRNAs in kinetoplastids. This small nuclear RNA is transcribed by RNA polymerase II from individual promoters. In Leishmania tarentolae the SL RNA genes reside in two multi-copy tandem arrays designated MINA and MINB. The transcript accumulation from the SL promoter on the drug-selected, episomal SL RNA gene cassette pX-tSL is ~10% that of the genomic array in uncloned L. tarentolae transfectants. This disparity is neither sequence- nor copy-number related, and thus may be due to interference of SL promoter function by epigenetic factors. To explore these possibilities we examined the nucleoplasmic localization of the SL RNA genes as well as their nucleosomal architecture.

Results
The genomic SL RNA genes and the episome did not co-localize within the nucleus. Each genomic repeat contains one nucleosome regularly positioned within the non-transcribed intergenic region. The 363-bp MINA array was resistant to micrococcal nuclease digestion between the -258 and -72 positions relative to the transcription start point due to nucleosome association, leaving the promoter elements and the entire transcribed region exposed for protein interactions. A pattern of ~164-bp protected segments was observed, corresponding to the amount of DNA typically bound by a nucleosome. By contrast, nucleosomes on the pX-tSL episome were randomly distributed over the episomal SL cassette, reducing transcription factor access to the episomal promoter by approximately 74%. Cloning of the episome transfectants revealed a range of transcriptional activities, implicating a mechanism of epigenetic heredity.

Conclusion
The disorganized nucleosomes on the pX episome are in a permissive conformation for transcription of the SL RNA cassette approximately 25% of the time within a given parasite. Nucleosome interference is likely the major factor in the apparent transcriptional repression of the SL RNA gene cassette. Coupled with the requirement for run-around transcription that drives expression of the selectable drug marker, transcription of the episomal SL may be reduced even further due to sub-optimal nucleoplasmic localization and initiation complex disruption.
Widespread pyocyanin over-production among isolates of a cystic fibrosis epidemic strain
Authors: Fothergill Joanne L , Panagea Stavroula , Hart Charles A , Walshaw Martin J , Pitt Tyrone L , Winstanley Craig 
Published: May 2007

Abstract

Background
Some isolates of the Liverpool cystic fibrosis epidemic strain of Pseudomonas aeruginosa exhibit an unusual virulence-related phenotype, characterized by over-production of quorum sensing-regulated exoproducts such as pyocyanin and LasA protease. Our aim was to determine the prevalence of this unusual phenotype amongst isolates of the epidemic strain, and to study other intraclonal phenotypic and genotypic variations.

Results
The unusual phenotype was detected in at least one epidemic strain isolate from the majority of cystic fibrosis patients tested, and can be retained for up to seven years during chronic infection. Multiple sequential isolates of the epidemic strain taken from six patients over a period of up to nine years exhibited a wide range of phenotypes, including different antimicrobial susceptibilities. Our data suggest that each sputum sample contains a mixture of phenotypes and genotypes within the epidemic strain population, including within colony morphotypes. Many isolates exhibit premature (during early rather than late exponential growth) and over-production of pyocyanin, which has a number of toxic effects directly relevant to cystic fibrosis.

Conclusion
The widespread occurrence of this unusual phenotype suggests that it may play an important role in the success of the epidemic strain.
Drug susceptibility testing of clinical isolates of streptococci and enterococci by the Phoenix automated microbiology system
Authors: Brigante Gioconda R , Luzzaro Francesco A , Pini Beatrice , Lombardi Gianluigi , Sokeng Gertrude , Toniolo Antonio Q 
Published: May 2007

Abstract

Background
Drug resistance is an emerging problem among streptococcal and enterococcal species. Automated diagnostic systems for species identification and antimicrobial susceptibility testing (AST) have become recently available. We evaluated drug susceptibility of clinical isolates of streptococci and enterococci using the recent Phoenix system (BD, Sparks, MD). Diagnostic tools included the new SMIC/ID-2 panel for streptococci, and the PMIC/ID-14 for enterococci. Two-hundred and fifty isolates have been investigated: β-hemolytic streptococci (n = 65), Streptococcus pneumoniae (n = 50), viridans group streptococci (n = 32), Enterococcus faecium (n = 40), Enterococcus faecalis (n = 43), other catalase-negative cocci (n = 20). When needed, species ID was determined using molecular methods. Test bacterial strains were chosen among those carrying clinically-relevant resistance determinants (penicillin, macrolides, fluoroquinolones, glycopeptides). AST results of the Phoenix system were compared to minimal inhibitory concentration (MIC) values measured by the Etest method (AB Biodisk, Solna, Sweden).

Results
Streptococci: essential agreement (EA) and categorical agreement (CA) were 91.9% and 98.8%, respectively. Major (ME) and minor errors (mE) accounted for 0.1% and 1.1% of isolates, respectively. No very major errors (VME) were produced. Enterococci: EA was 97%, CA 96%. Small numbers of VME (0.9%), ME (1.4%) and mE (2.8%) were obtained. Overall, EA and CA rates for most drugs were above 90% for both genera. A few VME were found: a) teicoplanin and high-level streptomycin for E. faecalis, b) high-level gentamicin for E. faecium. The mean time to results (± SD) was 11.8 ± 0.9 h, with minor differences between streptococci and enterococci.

Conclusion
The Phoenix system emerged as an effective tool for quantitative AST. Panels based on dilution tests provided rapid and accurate MIC values with regard to clinically-relevant streptococcal and enterococcal species.
Important roles of multiple Sp1 binding sites and epigenetic modifications in the regulation of the methionine sulfoxide reductase B1 (MsrB1) promoter
Authors: De Luca Antonella , Sacchetta Paolo , Nieddu Marzia , Di Ilio Carmine , Favaloro Bartolo 
Published: May 2007

Abstract

Background
Methionine sulfoxide reductases (Msrs) are enzymes that catalyze the reduction of oxidized methionine residues. Most organisms that were genetically modified to lack the MsrA gene have shown shortening of their life span. Methionine sulfoxide reductases B (MsrB) proteins codified by three separate genes, named MsrB1, MsrB2, and MsrB3, are included in the Msrs system. To date, the mechanisms responsible for the transcriptional regulation of MsrB genes have not been reported. The aim of this study was to investigate the regulation of MsrB1 selenoprotein levels through transcriptional regulation of the MsrB1 gene in MDA-MB231 and MCF-7 breast carcinoma cell lines.

Results
A MsrB1 gene promoter is located 169 base pairs upstream from the transcription start site. It contains three Sp1 binding sites which are sufficient for maximal promoter activity in transient transfection experiments.
High levels of MsrB1 transcript, protein and promoter activity were detected in low metastatic MCF7 human breast cancer cells. On the contrary, very low levels of both MsrB1 transcript and promoter activity were detected in the highly metastatic counterpart MDA-MB231 cells.
A pivotal role for Sp1 in the constitutive expression of the MsrB1 gene was demonstrated through transient expression of mutant MsrB1 promoter-reporter gene constructs and chromatin immunoprecipitation experiments.
Since Sp1 is ubiquitously expressed, these sites, while necessary, are not sufficient to explain the patterns of gene expression of MsrB1 in various human breast cancer cells. MDA-MB231 cells can be induced to express MsrB1 by treatment with 5-Aza-2'-deoxycytidine, a demethylating agent. Therefore, the MsrB1 promoter is controlled by epigenetic modifications.

Conclusion
The results of this study provide the first insights into the transcriptional regulation of the human MsrB1 gene, including the discovery that the Sp1 transcription factor may play a central role in its expression. We also demonstrated that the MsrB1 promoter activity appears to be controlled by epigenetic modifications such as methylation.