bluuebunny/crossref_metadata_2025_split huggingface dataset:
OligoRAP – an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity
Authors: Neerincx Pieter BT , Rauwerda Han , Nie Haisheng , Groenen Martien AM , Breit Timo M , Leunissen Jack AM 
Published: July 2009

Abstract

Background
High throughput gene expression studies using oligonucleotide microarrays depend on the specificity of each oligonucleotide (oligo or probe) for its target gene. However, target specific probes can only be designed when a reference genome of the species at hand were completely sequenced, when this genome were completely annotated and when the genetic variation of the sampled individuals were completely known. Unfortunately there is not a single species for which such a complete data set is available. Therefore, it is important that probe annotation can be updated frequently for optimal interpretation of microarray experiments.

Results
In this paper we present OligoRAP, a pipeline to automatically update the annotation of oligo libraries and estimate oligo target specificity. OligoRAP uses a reference genome assembly with Ensembl and Entrez Gene annotation supplemented with a set of unmapped transcripts derived from RefSeq and UniGene to handle assembly gaps. OligoRAP produces alignments of each oligo with the reference assembly as well as with unmapped transcripts. These alignments are re-mapped to the annotation sources, which results in a concise, as complete as possible and up-to-date annotation of the oligo library. The building blocks of this pipeline are BioMoby web services creating a highly modular and distributed system with a robust, remote programmatic interface.
OligoRAP was used to update the annotation for a subset of 791 oligos from the ARK-Genomics 20 K chicken array, which were selected as starting material for the oligo annotation session of the EADGENE/SABRE Post-analysis workshop. Based on the updated annotation about one third of these oligos is problematic with regard to target specificity. In addition, the accession numbers or ids the oligos were originally designed for no longer exist in the updated annotation for almost half of the oligos.

Conclusion
As microarrays are designed on incomplete data, it is important to update probe annotation and check target specificity regularly. OligoRAP provides both and due to its design based on BioMoby web services it can easily be embedded as an oligo annotation engine in customised applications for microarray data analysis. The dramatic difference in updated annotation and target specificity for the ARK-Genomics 20 K chicken array as compared to the original data emphasises the need for regular updates.
Gene set analysis methods applied to chicken microarray expression data
Authors: Skarman Axel , Jiang Li , Hornshøj Henrik , Buitenhuis Bart , Hedegaard Jakob , Conley Lene N , Sørensen Peter 
Published: July 2009

AbstractBackgroundGene set analysis is considered to be a way of improving our biological interpretation of the observed expression patterns. This paper describes different methods applied to analyse expression data from a chicken DNA microarray dataset.ResultsApplying different gene set analyses to the chicken expression data led to different ranking of the Gene Ontology terms tested. A method for prediction of possible annotations was applied.ConclusionBiological interpretation based on gene set analyses dependent on the statistical method used. Methods for predicting the possible annotations for genes with unknown function from the expression data at hand could be useful, but our results indicate that careful validation of the predictions is needed.
Abnormal social behavior, hyperactivity, impaired remote spatial memory, and increased D1-mediated dopaminergic signaling in neuronal nitric oxide synthase knockout mice
Authors: Tanda Koichi , Nishi Akinori , Matsuo Naoki , Nakanishi Kazuo , Yamasaki Nobuyuki , Sugimoto Tohru , Toyama Keiko , Takao Keizo , Miyakawa Tsuyoshi 
Published: July 2009

AbstractBackgroundNeuronal nitric oxide synthase (nNOS) is involved in the regulation of a diverse population of intracellular messenger systems in the brain. In humans, abnormal NOS/nitric oxide metabolism is suggested to contribute to the pathogenesis and pathophysiology of some neuropsychiatric disorders, such as schizophrenia and bipolar disorder. Mice with targeted disruption of the nNOS gene exhibit abnormal behaviors. Here, we subjected nNOS knockout (KO) mice to a battery of behavioral tests to further investigate the role of nNOS in neuropsychiatric functions. We also examined the role of nNOS in dopamine/DARPP-32 signaling in striatal slices from nNOS KO mice and the effects of the administration of a dopamine D1 receptor agonist on behavior in nNOS KO mice.ResultsnNOS KO mice showed hyperlocomotor activity in a novel environment, increased social interaction in their home cage, decreased depression-related behavior, and impaired spatial memory retention. In striatal slices from nNOS KO mice, the effects of a dopamine D1 receptor agonist, SKF81297, on the phosphorylation of DARPP-32 and AMPA receptor subunit GluR1 at protein kinase A sites were enhanced. Consistent with the biochemical results, intraperitoneal injection of a low dose of SKF81297 significantly decreased prepulse inhibition in nNOS KO mice, but not in wild-type mice.ConclusionThese findings indicate that nNOS KO upregulates dopamine D1 receptor signaling, and induces abnormal social behavior, hyperactivity and impaired remote spatial memory. nNOS KO mice may serve as a unique animal model of psychiatric disorders.
Methotrexate therapy associates with reduced prevalence of the metabolic syndrome in rheumatoid arthritis patients over the age of 60- more than just an anti-inflammatory effect? A cross sectional study
Authors: Toms Tracey E , Panoulas Vasileios F , John Holly , Douglas Karen MJ , Kitas George D 
Published: July 2009

AbstractIntroductionThe metabolic syndrome (MetS) may contribute to the excess cardiovascular burden observed in rheumatoid arthritis (RA). The prevalence and associations of the MetS in RA remain uncertain: systemic inflammation and anti-rheumatic therapy may contribute. Methotrexate (MTX) use has recently been linked to a reduced presence of MetS, via an assumed generic anti-inflammatory mechanism. We aimed to: assess the prevalence of the MetS in RA; identify factors that associate with its presence; and assess their interaction with the potential influence of MTX.MethodsMetS prevalence was assessed cross-sectionally in 400 RA patients, using five MetS definitions (National Cholesterol Education Programme 2004 and 2001, International Diabetes Federation, World Health Organisation and European Group for Study of Insulin Resistance). Logistic regression was used to identify independent predictors of the MetS. Further analysis established the nature of the association between MTX and the MetS.ResultsMetS prevalence rates varied from 12.1% to 45.3% in RA according to the definition used. Older age and higher HAQ scores associated with the presence of the MetS. MTX use, but not other disease modifying anti-rheumatic drugs (DMARDs) or glucocorticoids, associated with significantly reduced chance of having the MetS in RA (OR = 0.517, CI 0.33–0.81,P= 0.004).ConclusionsThe prevalence of the MetS in RA varies according to the definition used. MTX therapy, unlike other DMARDs or glucocorticoids, independently associates with a reduced propensity to MetS, suggesting a drug-specific mechanism, and makes MTX a good first-line DMARD in RA patients at high risk of developing the MetS, particularly those aged over 60 years.
Inducible expression of EVI1 in human myeloid cells causes phenotypes consistent with its role in myelodysplastic syndromes
Authors: Konrad Torsten A , Karger Anna , Hackl Hubert , Schwarzinger Ilse , Herbacek Irene , Wieser Rotraud 
Published: July 2009

Abstract
EVI1, a gene involved in myelodysplastic syndromes, causes growth arrest and cell death in U937 cells.
The oncogene EVI1 has been implicated in the etiology of AML and MDS. Although AML cells are characterized by accelerated proliferation and differentiation arrest, MDS cells hyperproliferate when immature but fail to differentiate later and die instead. In agreement with its roles in AML and in immature MDS cells, EVI1 was found to stimulate cell proliferation and inhibit differentiation in several experimental systems. In contrast, the variant protein MDS1/EVI1 caused the opposite effect in some of these assays. In the present study, we expressed EVI1 and MDS1/EVI1 in a tetracycline-regulable manner in the human myeloid cell line U937. Induction of either of these proteins caused cells to accumulate in the G0/G1-phase of the cell cycle and moderately increased the rate of spontaneous apoptosis. However, when EVI1- or MDS1/EVI1-expressing cells were induced to differentiate, they massively succumbed to apoptosis, as reflected by the accumulation of phosphatidylserine in the outer leaflet of the plasma membrane and increased rates of DNA fragmentation. In summary, these data show that inducible expression of EVI1 in U937 cells causes phenotypes that may be relevant for its role in MDS and provides a basis for further investigation of its contribution to this fatal disease.
Ca2+ signaling in airway epithelial cells facilitates leukocyte recruitment and transepithelial migration
Authors: Chun Jarin , Prince Alice 
Published: July 2009

AbstractReview on consequences of TLR2 signaling the activation of Ca2+-dependent proteases (calpains) and link to junctional proteins to facilitate PMN migration into the airway lumen.In airway cells, TLR2 stimulation by bacterial products activates Ca2+ fluxes that signal leukocyte recruitment to the lung and facilitates transepithelial migration into the airway lumen. TLR2 is apically displayed on airway cells, where it senses bacterial stimuli. Biochemical and genetic approaches demonstrate that TLR2 ligands stimulate release of Ca2+ from intracellular stores by activating TLR2 phosphorylation by c-Src and recruiting PI3K and PLCγ to affect Ca2+ release through IP3Rs. This Ca2+ release plays a pivotal role in signaling TLR2-dependent NF-κB activation and chemokine expression to recruit PMNs to the lung. In addition, TLR2-initiated Ca2+ release activates Ca2+-dependent proteases, calpains, which cleave the transmembrane proteins occludin and E-cadherin to promote PMN transmigration. This review highlights recent findings that demonstrate a central role for Ca2+ signaling in airway epithelial cells to induce proinflammatory gene transcription and to initiate junctional changes that accommodate transmigration of recruited PMNs.
Functional plasticity of macrophages: in situ reprogramming of tumor-associated macrophages
Authors: Stout Robert D , Watkins Stephanie K , Suttles Jill 
Published: July 2009

Abstract
Functionally polarized macrophages in chronic pathologies are highly adaptable cells displaying a functional response to tissue signals, which response can be reprogrammed to therapeutic advantage.
The extent to which the functional heterogeneity of Mφs is dependent on the differentiation of functional sublineages remains unresolved. One alternative hypothesis proposes that Mφs are functionally plastic cells, which are capable of altering their functional activities progressively in response to progressively changing signaling molecules generated in their microenvironment. This “functional plasticity” hypothesis predicts that the functionally polarized Mφs in chronic pathologies do not represent Mφ sublineages but rather, are mutable phenotypes sustained by chronic signaling from the pathological environment. Solid TAMφs are chronically polarized to provide activities that support tumor growth and metastasis and suppress adaptive immune responses. In support of the functional plasticity hypothesis, administration of slow-release microsphere-encapsulated IL-12 successfully reprogrammed TAMφs in situ, reducing Mφ support of tumor growth and metastasis and enhancing Mφ proimmunogenic activities. Increased knowledge of how Mφ function is regulated and how polarized Mφs can be reprogrammed in situ will increase our ability to control Mφ function in a variety of pathological states, including cancer and chronic inflammatory disease.
Up-regulation of alveolar macrophage matrix metalloproteinases in HIV1+ smokers with early emphysema
Authors: Kaner Robert J , Santiago Francisco , Crystal Ronald G 
Published: July 2009

Abstract
Increased production and activation of proteases by alveolar macrophages may contribute to the accelerated destruction of lung tissue in HIV-1+ smokers.
HIV1 + smokers develop emphysema at an earlier age and with a higher incidence than HIV1– smokers. Since human alveolar macrophages (AMs) are capable of producing proteases that degrade extracellular matrix components, we hypothesized that up-regulation of AM matrix metalloproteinases may be associated with the emphysema of HIV1+ smokers. Microarray analysis was used to screen which matrix metalloproteinases (MMPs) genes were expressed by AM of HIV1+ smokers with early emphysema. For each of the MMP genes expressed (MMP-1, −2, −7, −9, −10, −12 and −14), TaqMan PCR was used to quantify the relative expression in AM from four groups of individuals: HIV1– healthy nonsmokers, HIV1– healthy smokers, HIV1– smokers with early emphysema, and HIV1+ smokers with early emphysema. While AM gene expression of MMPs was higher in HIV1– individuals with emphysema in comparison with HIV1– healthy smokers, for the majority of the MMPs (−1, −7, −9, and −12), AM expression from HIV1+ smokers with early emphysema was significantly higher than in HIV1− smokers with early emphysema. HIV1+ individuals with early emphysema also had higher levels of epithelial lining fluid (ELF) MMPs (−2, −7, −9, and −12) than the 3 HIV1− groups. ELF MMP (−2,-7,-9, and −12) levels were similar in HIV1+ nonsmokers compared with HIV1− nonsmokers. Interestingly, the active forms of MMP-2, −9, and −12 were exclusively detected in ELF from HIV1+ individuals with early emphysema. Since the activities of the up-regulated AM MMPs include collagenases, gelatinases, matrilysins, and elastase, these data suggest that up-regulated AM MMP genes and activation of MMP proteins may contribute to the emphysema of HIV1+ individuals who smoke.
The Transformation of Traditional Woodland Management: Commercial Sylviculture in Medieval Champagne
Authors: Keyser Richard 
Published: July 2009

This essay argues that high medieval economic growth in Champagne and elsewhere in northern France encouraged a switch in the primary focus of woodland management from extensive silvo-pastoralism to intensive small wood production. For the first time in the thirteenth century, coppicing, short cycles of cutting and regeneration of trees capable of resprouting from stumps or trunks, came to dominate sylviculture as an intensively managed, market-oriented system, one that lasted for centuries. This essay thus provides a wider context for the late medieval and early modern French state's role in shaping forest exploitation. Royal officials did not so much innovate as respond to new market opportunities by appropriating and generalizing practices that had long existed in many regions. Before the sixteenth century few educated experts ventured into the details of woodland management, which remained largely the preserve of nonelite peasants, foresters, and woodmongers, the bearers of a traditional, orally transmitted ecological knowledge.
Cet essai soutient qu'en Champagne et ailleurs dans la France du Nord la croissance économique du Moyen Age classique a encouragé un changement dans l'exploitation forestière du pastoralisme extensif à la production intensive du bois. Pour la première fois au treizième siècle le bois taillis, la coupe rapprochée des arbres capables de rejeter des souches, a dominé la sylviculture en système organisé pour le marché et ce-là persistera pour des siècles. Cet essai donne ainsi un contexte plus large au rôle de l'Etat Français tardo-médiévale et moderne dans le modelage de l'exploitation forestière. Les fonctionnaires royaux ont moins innové que réagi aux nouvelles opportunités commerciales par l'appropriation et la généralisation des pratiques qui existaient depuis longtemps. Jusqu'au seizième siècle, peu de spécialistes formés à l'université ont abordé l'exploitation forestière, qui est restée principalement le domaine des simples paysans, forestiers, et marchands, porteurs d'un savoir écologique populaire.
To Historicize or Naturalize Nature: Hydraulic Communities and Administrative States in Nineteenth-Century Europe
Authors: Ingold Alice 
Published: July 2009

This article focuses on the discourses related to the management of water resources occurring in several regions of Europe after the French Revolution. Written by agronomists, engineers, and lawyers, these texts point to hydraulic societies. The writings of two authors are analyzed: those of François-Jacques Jaubert de Passa in France and those of Carlo Cattaneo in Italy. They refer to political and legal institutions and to systems of knowledge that were alternative to those put in place by the administrative states. They presented irrigation systems as edifices created over a long period of time: benefiting from empirical practices and from a technical culture that represented an alternative to that of state engineers, these edifices emerged as the expression of an equilibrium between society and its environment. In contrast to this narrative, state engineers transmitted a naturalized vision of water to support the claims of states on these resources. I argue that the nineteenth century corresponds with a face-to-face vision of nature, the historical one versus the natural one.
Cet article identifie une série de textes sur le gouvernement du territoire et des eaux qui paraissent après la Révolution française dans plusieurs régions d'Europe. Ces textes défendent des institutions politiques et juridiques et des dispositifs de savoirs alternatifs à ceux mis alors en place par les Etats administratifs. L'analyse porte sur deux auteurs qui décrivent des sociétés hydrauliques: François-Jacques Jaubert de Passa en France et Carlo Cattaneo en Italie présentent les systèmes irrigués comme des édifices élaborés dans la très longue durée. Construits à la faveur de pratiques et d'une culture technique alternative à celle des ingénieurs d'Etat, ces édifices apparaissent comme l'expression d'un équilibre entre une société et son environnement. En historicisant ces descriptions ethnographiques, le contexte de leur élaboration et de leur circulation, cet article propose d'identifier les tensions qui s'expriment dans un long dixneuvième siècle entre des définitions alternatives de la nature, une nature historicisée et socialisée et une nature naturalisée, ouvrant chacune à des formes politiques et à des systèmes de droits différents.
The Natures of Nation: Negotiating Modernity in the Landes de Gascogne
Authors: Temple Samuel 
Published: July 2009

This article examines the transformation of the Landes de Gascogne in southwestern France. Once dominated by a sparse agropastoral landscape, the region underwent an intense program of pine forestation in the second half of the nineteenth century. The engineered forest, however, quickly escaped the grasp of the administrators, engineers, and local property owners who helped create it. Catastrophic fires plagued the monoculture pine stands, and by the end of the 1940s almost half of the woodlands had been destroyed. By focusing on the complex conflicts and negotiations that marked the origins of the Landais forests, this article presents a case study in the environmental dimensions of state making in modern France. It demonstrates how local and state claims over, first, the pastoral landes and, later, the industrial woodlands, prove difficult to disentangle and suggests the importance of an ambivalent discourse of marginality to the exercise and negotiation of authority in the modern nation-state.
Cet article examine la transformation des Landes de Gascogne, une région qui s'étend sur trois départements du sud-ouest de la France. Jadis couverte de vastes landes qui soutenaient une société agropastorale, la campagne s'était transformée par le boisement des pins après 1850, un grand projet amorcé par le gouvernement du Second Empire. Cependant, la nouvelle forêt a échappé rapidement à l'emprise de ses créateurs: les administrateurs, les ingénieurs et les propriétaires. Frappée par une série d'incendies catastrophiques, presque la moitié de la forêt se trouva détruite à la fin des années 1940. A travers une étude des origines des forêts, cet article offre une analyse du rôle de l'environnement dans l'étatisation en France. L'article montre que les revendications locales et nationales sur, d'abord, les landes pastorales, et plus tard, la forêt industrielle, s'avéraient difficiles à démêler. Un discours de marginalité a été essentiel à la pratique et à la négociation d'autorité dans l'Etat-nation moderne.
A Tasteful Patrimony? Landscape Preservation and Tourism in the Sites and Monuments Campaign, 1900–1935
Authors: Young Patrick 
Published: July 2009

This article analyzes the Touring Club de France's Sites and Monuments campaign as a nationwide initiative to define and secure the value of natural landscapes in the face of accelerated economic change in rural France. In its work of inventorying, representation, and associational intervention in Brittany, I argue, the campaign formalized recognition of both a national and tourist interest vis-à-vis the Breton natural landscape; the ethos of bourgeois stewardship (of national resources, regional identity, and taste) that it propagated, though, coexisted uneasily at specific sites with more local usages and dispositions. The effort to reconstitute the Breton (and French) natural environments failed ultimately to secure the value and meaning of landscapes as preservationists had intended. Recast as a patrimony and domain of consumption, that natural environment now played host to multiple and sometimes contradictory appropriations.
En traitant du projet de conservation « sites et monuments », cet article analyse l'effet du tourisme sur l'environnement naturel en France, particulièrement en Bretagne pendant l'entre-deux-guerres. Ce projet d'association et d'intervention a rassemblé un grand nombre de bourgeois (notamment dans les associations protectionnistes et touristiques) se donnant pour mission de faire reconnaître et de sauvegarder la valeur des paysages français. L'analyse des rapports d'activités d'organisations de protection et du tourisme, d'ouvrages consacrés au tourisme et des photographies de sites révèle les liens intimes entre l'idée de préservation et l'identité et les aspirations d'une couche sociale en voie de développement sous la Troisième République. Dans leur travail d'inventaire, d'action associative et de représentation des sites et monuments naturels, les partisans de la conservation ont largement assuré la reconnaissance d'un intérêt national et touristique pour le paysage. De plus, ils se sont imposés comme les protecteurs exclusifs du patrimoine régional et national et du bon goût.