bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perception de quelques mécanismes favorables à la réduction des inégalités sociales de santé en France
Authors: Ridde Valéry , Guichard Anne 
Published: August 2011

Résumé La promotion de la santé peine à faire la démonstration de sa capacité à réduire les inégalités sociales de santé. Cette recherche exploratoire utilise la démarche de l’ évaluation réaliste pour identifier au sein de cinq actions, les mécanismes favorables à la réduction des inégalités sociales de santé en France. Des études de cas ont été effectuées à partir de cinq actions de promotion de la santé dans trois régions. Les données proviennent de 41 entrevues individuelles et de la documentation des actions. Les entrevues ont été conduites pour explorer une liste de 51 mécanismes candidats sélectionnés à partir de trois outils tirés de la littérature. L’analyse des données a été réalisée au moyen d’une analyse de contenu. Les mécanismes suivants ont été confirmés par cette étude empirique : implication de tous les partenaires clés, participation significative, valorisation des différents types d’apports et de savoirs, vision commune, leadership partagé, réflexion critique continue sur les processus et les résultats, mobilisation de ressources. Cette recherche exploratoire a permis de confirmer, par des données empiriques, l’existence de ce mécanismes spécifiques aux actions visant la réduction des inégalités sociales de santé selon le point de vue des acteurs. En même temps, elle a été en mesure de révéler de nouveaux mécanismes candidats dont l’exploration doit être poursuivie lors de nouvelles recherches. L’analyse montre cependant qu’il ne faut pas uniquement se focaliser sur les mécanismes mais aussi considérer largement le rôle des entrepreneurs politiques dans la réussite des actions. Cette recherche exploratoire montre que la démarche de l’ évaluation réaliste est faisable, mais il conviendrait de la reproduire à une plus grande échelle pour accéder à l’ensemble des connaissances nécessaires à une compréhension plus exhaustive des mécanismes favorables à la réduction des inégalités sociales de santé en France.
Effect of genetic polymorphisms on the development of secondary failure to sulfonylurea in Egyptian patients with type 2 diabetes
Authors: El-sisi Alaa E. , Hegazy Sahar K. , Metwally Shereen S. , Wafa Alaa M. , Dawood Naglaa A. 
Published: August 2011

Objective: This study investigated the possibility that genetic factors, such as polymorphism of K inward rectifier subunit (Kir6.2), E23K, and Arg972 polymorphism of insulin receptor substrate-1 (IRS-1), may predispose patients to sulfonylurea failure. Methods: A total of 100 unrelated Egyptian patients with type 2 diabetes were recruited. They were divided into two equal groups: group I consisted of patients with secondary failure to sulfonylurea (hemoglobin A1c ≥ 8% despite sulfonylurea therapy) while group II consisted of patients whose condition was controlled with oral therapy. Results: Of all the patients, 45% and 14% were carriers of the K allele and Arg972 variants respectively. The frequency of the K allele was 34% among patients with diabetes that was controlled with oral therapy and 56% among patients with secondary failure to sulfonylurea. The frequency of the Arg972 IRS-1 variant was 6% among patients with diabetes controlled with oral therapy and 22% among patients with secondary failure. Conclusion: The E23K variant of the Kir6.2 gene and Arg972 IRS-1 variants are associated with increased risk for secondary failure to sulfonylurea.
Immunologic effects of rituximab on the human spleen in immune thrombocytopenia
Authors: Audia Sylvain , Samson Maxime , Guy Julien , Janikashvili Nona , Fraszczak Jennifer , Trad Malika , Ciudad Marion , Leguy Vanessa , Berthier Sabine , Petrella Tony , Aho-Glélé Serge , Martin Laurent , Maynadié Marc , Lorcerie Bernard , Rat Patrick , Cheynel Nicolas , Katsanis Emmanuel , Larmonier Nicolas , Bonnotte Bernard 
Published: August 2011

AbstractImmune thrombocytopenia (ITP) is an autoimmune disease with a complex pathogenesis. As in many B cell–related autoimmune diseases, rituximab (RTX) has been shown to increase platelet counts in some ITP patients. From an immunologic standpoint, the mode of action of RTX and the reasons underlying its limited efficacy have yet to be elucidated. Because splenectomy is a cornerstone treatment of ITP, the immune effect of RTX on this major secondary lymphoid organ was investigated in 18 spleens removed from ITP patients who were treated or not with RTX. Spleens from ITP individuals had follicular hyperplasia consistent with secondary follicles. RTX therapy resulted in complete B-cell depletion in the blood and a significant reduction in splenic B cells, but these patients did not achieve remission. Moreover, whereas the percentage of circulating regulatory T cells (Tregs) was similar to that in controls, splenic Tregs were reduced in ITP patients. Interestingly, the ratio of proinflammatory Th1 cells to suppressive Tregs was increased in the spleens of patients who failed RTX therapy. These results indicate that although B cells are involved in ITP pathogenesis, RTX-induced total B-cell depletion is not correlated with its therapeutic effects, which suggests additional immune-mediated mechanisms of action of this drug.
Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics
Authors: Chepelev Leonid L , Riazanov Alexandre , Kouznetsov Alexandre , Low Hong Sang , Dumontier Michel , Baker Christopher JO 
Published: August 2011

Abstract

Background
The development of high-throughput experimentation has led to astronomical growth in biologically relevant lipids and lipid derivatives identified, screened, and deposited in numerous online databases. Unfortunately, efforts to annotate, classify, and analyze these chemical entities have largely remained in the hands of human curators using manual or semi-automated protocols, leaving many novel entities unclassified. Since chemical function is often closely linked to structure, accurate structure-based classification and annotation of chemical entities is imperative to understanding their functionality.

Results
As part of an exploratory study, we have investigated the utility of semantic web technologies in automated chemical classification and annotation of lipids. Our prototype framework consists of two components: an ontology and a set of federated web services that operate upon it. The formal lipid ontology we use here extends a part of the LiPrO ontology and draws on the lipid hierarchy in the LIPID MAPS database, as well as literature-derived knowledge. The federated semantic web services that operate upon this ontology are deployed within the Semantic Annotation, Discovery, and Integration (SADI) framework. Structure-based lipid classification is enacted by two core services. Firstly, a structural annotation service detects and enumerates relevant functional groups for a specified chemical structure. A second service reasons over lipid ontology class descriptions using the attributes obtained from the annotation service and identifies the appropriate lipid classification. We extend the utility of these core services by combining them with additional SADI services that retrieve associations between lipids and proteins and identify publications related to specified lipid types. We analyze the performance of SADI-enabled eicosanoid classification relative to the LIPID MAPS classification and reflect on the contribution of our integrative methodology in the context of high-throughput lipidomics.

Conclusions
Our prototype framework is capable of accurate automated classification of lipids and facile integration of lipid class information with additional data obtained with SADI web services. The potential of programming-free integration of external web services through the SADI framework offers an opportunity for development of powerful novel applications in lipidomics. We conclude that semantic web technologies can provide an accurate and versatile means of classification and annotation of lipids.
Applications of the pipeline environment for visual informatics and genomics computations
Authors: Dinov Ivo D , Torri Federica , Macciardi Fabio , Petrosyan Petros , Liu Zhizhong , Zamanyan Alen , Eggert Paul , Pierce Jonathan , Genco Alex , Knowles James A , Clark Andrew P , Van Horn John D , Ames Joseph , Kesselman Carl , Toga Arthur W 
Published: August 2011

Abstract

Background
Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analysis-protocol provenance. The Pipeline is a client-server distributed computational environment that facilitates the visual graphical construction, execution, monitoring, validation and dissemination of advanced data analysis protocols.

Results
This paper reports on the applications of the LONI Pipeline environment to address two informatics challenges - graphical management of diverse genomics tools, and the interoperability of informatics software. Specifically, this manuscript presents the concrete details of deploying general informatics suites and individual software tools to new hardware infrastructures, the design, validation and execution of new visual analysis protocols via the Pipeline graphical interface, and integration of diverse informatics tools via the Pipeline eXtensible Markup Language syntax. We demonstrate each of these processes using several established informatics packages (e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie) for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of bioinformatics resources which provide a well-defined syntax for dynamic specification of the input/output parameters and the run-time execution controls.

Conclusions
The LONI Pipeline environment http://pipeline.loni.ucla.edu provides a flexible graphical infrastructure for efficient biomedical computing and distributed informatics research. The interactive Pipeline resource manager enables the utilization and interoperability of diverse types of informatics resources. The Pipeline client-server model provides computational power to a broad spectrum of informatics investigators - experienced developers and novice users, user with or without access to advanced computational-resources (e.g., Grid, data), as well as basic and translational scientists. The open development, validation and dissemination of computational networks (pipeline workflows) facilitates the sharing of knowledge, tools, protocols and best practices, and enables the unbiased validation and replication of scientific findings by the entire community.
Plasticity of photoreceptor-generating retinal progenitors revealed by prolonged retinoic acid exposure
Authors: Stevens Craig B , Cameron David A , Stenkamp Deborah L 
Published: August 2011

Abstract

Background
Retinoic acid (RA) is important for vertebrate eye morphogenesis and is a regulator of photoreceptor development in the retina. In the zebrafish, RA treatment of postmitotic photoreceptor precursors has been shown to promote the differentiation of rods and red-sensitive cones while inhibiting the differentiation of blue- and UV-sensitive cones. The roles played by RA and its receptors in modifying photoreceptor fate remain to be determined.

Results
Treatment of zebrafish embryos with RA, beginning at the time of retinal progenitor cell proliferation and prior to photoreceptor terminal mitosis, resulted in a significant alteration of rod and cone mosaic patterns, suggesting an increase in the production of rods at the expense of red cones. Quantitative pattern analyses documented increased density of rod photoreceptors and reduced local spacing between rod cells, suggesting rods were appearing in locations normally occupied by cone photoreceptors. Cone densities were correspondingly reduced and cone photoreceptor mosaics displayed expanded and less regular spacing. These results were consistent with replacement of approximately 25% of positions normally occupied by red-sensitive cones, with additional rods. Analysis of embryos from a RA-signaling reporter line determined that multiple retinal cell types, including mitotic cells and differentiating rods and cones, are capable of directly responding to RA. The RA receptors RXRγ and RARαb are expressed in patterns consistent with mediating the effects of RA on photoreceptors. Selective knockdown of RARαb expression resulted in a reduction in endogenous RA signaling in the retina. Knockdown of RARαb also caused a reduced production of rods that was not restored by simultaneous treatments with RA.

Conclusions
These data suggest that developing retinal cells have a dynamic sensitivity to RA during retinal neurogenesis. In zebrafish RA may influence the rod vs. cone cell fate decision. The RARαb receptor mediates the effects of endogenous, as well as exogenous RA, on rod development.
A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing
Authors: Meylan Sylvain , Groner Anna C , Ambrosini Giovanna , Malani Nirav , Quenneville Simon , Zangger Nadine , Kapopoulou Adamandia , Kauzlaric Annamaria , Rougemont Jacques , Ciuffi Angela , Bushman Frederic D , Bucher Philipp , Trono Didier 
Published: August 2011

Abstract

Background
KRAB-ZFPs (Krüppel-associated box domain-zinc finger proteins) are vertebrate-restricted transcriptional repressors encoded in the hundreds by the mouse and human genomes. They act via an essential cofactor, KAP1, which recruits effectors responsible for the formation of facultative heterochromatin. We have recently shown that KRAB/KAP1 can mediate long-range transcriptional repression through heterochromatin spreading, but also demonstrated that this process is at times countered by endogenous influences.

Method
To investigate this issue further we used an ectopic KRAB-based repressor. This system allowed us to tether KRAB/KAP1 to hundreds of euchromatic sites within genes, and to record its impact on gene expression. We then correlated this KRAB/KAP1-mediated transcriptional effect to pre-existing genomic and chromatin structures to identify specific characteristics making a gene susceptible to repression.

Results
We found that genes that were susceptible to KRAB/KAP1-mediated silencing carried higher levels of repressive histone marks both at the promoter and over the transcribed region than genes that were insensitive. In parallel, we found a high enrichment in euchromatic marks within both the close and more distant environment of these genes.

Conclusion
Together, these data indicate that high levels of gene activity in the genomic environment and the pre-deposition of repressive histone marks within a gene increase its susceptibility to KRAB/KAP1-mediated repression.
Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice
Authors: Coudert Yoan , Bès Martine , Van Anh Le Thi , Pré Martial , Guiderdoni Emmanuel , Gantet Pascal 
Published: August 2011

Abstract

Background
In rice, the major part of the post-embryonic root system is made of stem-derived roots named crown roots (CR). Among the few characterized rice mutants affected in root development, crown rootless1 mutant is unable to initiate crown root primordia. CROWN ROOTLESS1 (CRL1) is induced by auxin and encodes an AS2/LOB-domain transcription factor that acts upstream of the gene regulatory network controlling CR development.

Results
To identify genes involved in CR development, we compared global gene expression profile in stem bases of crl1 mutant and wild-type (WT) plants. Our analysis revealed that 250 and 236 genes are down- and up-regulated respectively in the crl1 mutant. Auxin induces CRL1 expression and consequently it is expected that auxin also alters the expression of genes that are early regulated by CRL1. To identify genes under the early control of CRL1, we monitored the expression kinetics of a selected subset of genes, mainly chosen among those exhibiting differential expression, in crl1 and WT following exogenous auxin treatment. This analysis revealed that most of these genes, mainly related to hormone, water and nutrient, development and homeostasis, were likely not regulated directly by CRL1. We hypothesized that the differential expression for these genes observed in the crl1 mutant is likely a consequence of the absence of CR formation. Otherwise, three CRL1- dependent auxin-responsive genes: FSM (FLATENNED SHOOT MERISTEM)/FAS1 (FASCIATA1), GTE4 (GENERAL TRANSCRIPTION FACTOR GROUP E4) and MAP (MICROTUBULE-ASSOCIATED PROTEIN) were identified. FSM/FAS1 and GTE4 are known in rice and Arabidopsis to be involved in the maintenance of root meristem through chromatin remodelling and cell cycle regulation respectively.

Conclusion
Our data showed that the differential regulation of most genes in crl1 versus WT may be an indirect consequence of CRL1 inactivation resulting from the absence of CR in the crl1 mutant. Nevertheless some genes, FAS1/FSM, GTE4 and MAP, require CRL1 to be induced by auxin suggesting that they are likely directly regulated by CRL1. These genes have a function related to polarized cell growth, cell cycle regulation or chromatin remodelling. This suggests that these genes are controlled by CRL1 and involved in CR initiation in rice.
A multi locus variable number of tandem repeat analysis (MLVA) scheme for Streptococcus agalactiae genotyping
Authors: Haguenoer Eve , Baty Gaelle , Pourcel Christine , Lartigue Marie-Frédérique , Domelier Anne-Sophie , Rosenau Agnès , Quentin Roland , Mereghetti Laurent , Lanotte Philippe 
Published: August 2011

Abstract

Background
Multilocus sequence typing (MLST) is currently the reference method for genotyping Streptococcus agalactiae strains, the leading cause of infectious disease in newborns and a major cause of disease in immunocompromised children and adults. We describe here a genotyping method based on multiple locus variable number of tandem repeat (VNTR) analysis (MLVA) applied to a population of S. agalactiae strains of various origins characterized by MLST and serotyping.

Results
We studied a collection of 186 strains isolated from humans and cattle and three reference strains (A909, NEM316 and 2603 V/R). Among 34 VNTRs, 6 polymorphic VNTRs loci were selected for use in genotyping of the bacterial population. The MLVA profile consists of a series of allele numbers, corresponding to the number of repeats at each VNTR locus. 98 MLVA genotypes were obtained compared to 51 sequences types generated by MLST. The MLVA scheme generated clusters which corresponded well to the main clonal complexes obtained by MLST. However it provided a higher discriminatory power. The diversity index obtained with MLVA was 0.960 compared to 0.881 with MLST for this population of strains.

Conclusions
The MLVA scheme proposed here is a rapid, cheap and easy genotyping method generating results suitable for exchange and comparison between different laboratories and for the epidemiologic surveillance of S. agalactiae and analyses of outbreaks.
Genotypic and phenotypic diversity of Ralstonia pickettii and Ralstonia insidiosa isolates from clinical and environmental sources including High-purity Water. Diversity in Ralstonia pickettii
Authors: Ryan Michael P , Pembroke J Tony , Adley Catherine C 
Published: August 2011

Abstract

Background

Ralstonia pickettii is a nosocomial infectious agent and a significant industrial contaminant. It has been found in many different environments including clinical situations, soil and industrial High Purity Water. This study compares the phenotypic and genotypic diversity of a selection of strains of Ralstonia collected from a variety of sources.

Results

Ralstonia isolates (fifty-nine) from clinical, industrial and environmental origins were compared genotypically using i) Species-specific-PCR, ii) PCR and sequencing of the 16S-23S rRNA Interspatial region (ISR) iii) the fliC gene genes, iv) RAPD and BOX-PCR and v) phenotypically using biochemical testing. The species specific-PCR identified fifteen out of fifty-nine designated R. pickettii isolates as actually being the closely related species R. insidiosa. PCR-ribotyping of the 16S-23S rRNA ISR indicated few major differences between the isolates. Analysis of all isolates demonstrated different banding patterns for both the RAPD and BOX primers however these were found not to vary significantly.

Conclusions

R. pickettii species isolated from wide geographic and environmental sources appear to be reasonably homogenous based on genotypic and phenotypic characteristics. R. insidiosa can at present only be distinguished from R. pickettii using species specific PCR. R. pickettii and R. insidiosa isolates do not differ significantly phenotypically or genotypically based on environmental or geographical origin.
Elective surgical referral guidelines - background educational material or essential shared decision making tool? A survey of GPs' in England
Authors: Blundell Naomi , Taylor-Phillips Sian , Spitzer David , Martin Steven , Forde Ian , Clarke Aileen 
Published: August 2011

Abstract

Background
To investigate general practitioners' (GPs') attitudes to guidelines for elective surgical referral in England. To understand their use of guidelines, and attitudes to shared decision making in the referral decision.

Methods
A questionnaire was developed which investigated attitudes to and use of guidelines. It was given to a stratified random sample 30% (n = 310) drawn from GP lists of 10 English health districts (primary care trusts (PCTs)). GPs were invited to respond online, by telephone, fax or post. Data were analysed using descriptive statistics and backwards stepwise logistic regression.

Results
Responses were representative of GPs in England, but (despite up to 6 contacts per non-responder) the overall response rate was 41.6% (n = 129; with the range across PCTs of 25-61%). Most responding GPs indicated support for referral guidelines but 18% reported that they had never used them. Less than three per cent reported use for most or all referral decisions. The odds of using guidelines decreased with increasing age, with a ten year increase in age associated with halving odds of use (OR = 0.53, 95%CI = 0.29-0.90). Over 50% of GPs wanted good access to electronic guidelines with expert information and advice on guideline availability. Almost all (>89%) GPs agreed with sharing referral decisions with patients. Female doctors (OR = 5.2, 95%CI: 1.02-26.3) were more likely to agree with this than male GPs as were those working in larger compared to small or single handed practices (OR = 5.3, 95%CI: 1.4-19.9).

Conclusions
This group of responding GPs was supportive of guidelines but used them in different ways. Referral guidelines should have an educational component for background reading; include key messages for internalisation and application; and incorporate mechanisms to facilitate accessibility and appropriate shared decision making with patients.