777 research outputs found
Object Serialization and Deserialization Using XML
Interoperability of potentially heterogeneous databases has been an ongoing
research issue for a number of years in the database community. With the trend
towards globalization of data location and data access and the consequent
requirement for the coexistence of new data stores with legacy systems, the
cooperation and data interchange between data repositories has become
increasingly important. The emergence of the eXtensible Markup Language (XML)
as a database independent representation for data offers a suitable mechanism
for transporting data between repositories. This paper describes a research
activity within a group at CERN (called CMS) towards identifying and
implementing database serialization and deserialization methods that can be
used to replicate or migrate objects across the network between CERN and
worldwide centres using XML to serialize the contents of multiple objects
resident in object-oriented databases.Comment: 14 pages 7 figure
Higher-order non-symmetric counterterms in pure Yang-Mills theory
We analyze the restoration of the Slavnov-Taylor (ST) identities for pure
massless Yang-Mills theory in the Landau gauge within the BPHZL renormalization
scheme with IR regulator. We obtain the most general form of the action-like
part of the symmetric regularized action, obeying the relevant ST identities
and all other relevant symmetries of the model, to all orders in the loop
expansion. We also give a cohomological characterization of the fulfillment of
BPHZL IR power-counting criterion, guaranteeing the existence of the limit
where the IR regulator goes to zero. The technique analyzed in this paper is
needed in the study of the restoration of the ST identities for those models,
like the MSSM, where massless particles are present and no invariant
regularization scheme is known to preserve the full set of ST identities of the
theory.Comment: Final version published in the journa
Distributed Computing Grid Experiences in CMS
The CMS experiment is currently developing a computing system capable of serving, processing and archiving the large number of events that will be generated when the CMS detector starts taking data. During 2004 CMS undertook a large scale data challenge to demonstrate the ability of the CMS computing system to cope with a sustained data-taking rate equivalent to 25% of startup rate. Its goals were: to run CMS event reconstruction at CERN for a sustained period at 25 Hz input rate; to distribute the data to several regional centers; and enable data access at those centers for analysis. Grid middleware was utilized to help complete all aspects of the challenge. To continue to provide scalable access from anywhere in the world to the data, CMS is developing a layer of software that uses Grid tools to gain access to data and resources, and that aims to provide physicists with a user friendly interface for submitting their analysis jobs. This paper describes the data challenge experience with Grid infrastructure and the current development of the CMS analysis system
Anomalously large oxygen-ordering contribution to the thermal expansion of untwinned YBa2Cu3O6.95 single crystals: a glass-like transition near room temperature
We present high-resolution capacitance dilatometry studies from 5 - 500 K of
untwinned YBa2Cu3Ox (Y123) single crystals for x ~ 6.95 and x = 7.0. Large
contributions to the thermal expansivities due to O-ordering are found for x ~
6.95, which disappear below a kinetic glass-like transition near room
temperature. The kinetics at this glass transition is governed by an energy
barrier of 0.98 +- 0.07 eV, in very good agreement with other O-ordering
studies. Using thermodynamic arguments, we show that O-ordering in the Y123
system is particularly sensitive to uniaxial pressure (stress) along the chain
axis and that the lack of well-ordered chains in Nd123 and La123 is most likely
a consequence of a chemical-pressure effect.Comment: 4 pages, 3 figures, submitted to PR
Activation of the aryl hydrocarbon receptor dampens the severity of inflammatory skin conditions
Environmental stimuli are known to contribute to psoriasis pathogenesis and that of other autoimmune diseases, but the mechanisms are largely unknown. Here we show that the aryl hydrocarbon receptor (AhR), a transcription factor that senses environmental stimuli, modulates pathology in psoriasis. AhR-activating ligands reduced inflammation in the lesional skin of psoriasis patients, whereas AhR antagonists increased inflammation. Similarly, AhR signaling via the endogenous ligand FICZ reduced the inflammatory response in the imiquimod-induced model of skin inflammation and AhR-deficient mice exhibited a substantial exacerbation of the disease, compared to AhR-sufficient controls. Nonhematopoietic cells, in particular keratinocytes, were responsible for this hyperinflammatory response, which involved upregulation of AP-1 family members of transcription factors. Thus, our data suggest a critical role for AhR in the regulation of inflammatory responses and open the possibility for novel therapeutic strategies in chronic inflammatory disorders
Revealing natural relationships among arbuscular mycorrhizal fungi: culture line BEG47 represents Diversispora epigaea, not Glomus versiforme
Background: Understanding the mechanisms underlying biological phenomena, such as evolutionarily conservative trait inheritance, is predicated on knowledge of the natural relationships among organisms. However, despite their enormous ecological significance, many of the ubiquitous soil inhabiting and plant symbiotic arbuscular mycorrhizal fungi (AMF, phylum Glomeromycota) are incorrectly classified.
Methodology/Principal Findings:
Here, we focused on a frequently used model AMF registered as culture BEG47. This fungus is a descendent of the ex-type culture-lineage of Glomus epigaeum, which in 1983 was synonymised with Glomus versiforme. It has since then been used as âG. versiforme BEG47â. We show by morphological comparisons, based on type material, collected 1860â61, of G. versiforme and on type material and living ex-type cultures of G. epigaeum, that these two AMF species cannot be conspecific, and by molecular phylogenetics that BEG47 is a member of the genus Diversispora.
Conclusions: This study highlights that experimental works published during the last >25 years on an AMF named âG. versiformeâ or âBEG47â refer to D. epigaea, a species that is actually evolutionarily separated by hundreds of millions of years from all members of the genera in the Glomerales and thus from most other commonly used AMF âlaboratory strainsâ. Detailed redescriptions substantiate the renaming of G. epigaeum (BEG47) as D. epigaea, positioning it systematically in the order Diversisporales, thus enabling an evolutionary understanding of genetical, physiological, and ecological traits, relative to those of other AMF. Diversispora epigaea is widely cultured as a laboratory strain of AMF, whereas G. versiforme appears not to have been cultured nor found in the field since its original description
T Cell Activation Results in Conformational Changes in the Src Family Kinase Lck to Induce Its Activation
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Late activation of the 9-oxylipin pathway during arbuscular mycorrhiza formation in tomato and its regulation by jasmonate signalling
The establishment of an arbuscular mycorrhizal (AM) symbiotic interaction is a successful strategy for the promotion of substantial plant growth, development, and fitness. Numerous studies have supported the hypothesis that plant hormones play an important role in the establishment of functional AM symbiosis. Particular attention has been devoted to jasmonic acid (JA) and its derivates, which are believed to play a major role in AM symbiosis. Jasmonates belong to a diverse class of lipid metabolites known as oxylipins that include other biologically active molecules. Recent transcriptional analyses revealed up-regulation of the oxylipin pathway during AM symbiosis in mycorrhizal tomato roots and indicate a key regulatory role for oxylipins during AM symbiosis in tomato, particularly those derived from the action of 9-lipoxygenases (9-LOXs). Continuing with the tomato as a model, the spatial and temporal expression pattern of genes involved in the 9-LOX pathway during the different stages of AM formation in tomato was analysed. The effects of JA signalling pathway changes on AM fungal colonization were assessed and correlated with the modifications in the transcriptional profiles of 9-LOX genes. The up-regulation of the 9-LOX oxylipin pathway in mycorrhizal wild-type roots seems to depend on a particular degree of AM fungal colonization and is restricted to the colonized part of the roots, suggesting that these genes could play a role in controlling fungal spread in roots. In addition, the results suggest that this strategy of the plant to control AM fungi development within the roots is at least partly dependent on JA pathway activation
TRAL: tandem repeat annotation library.
MOTIVATION: Currently, more than 40 sequence tandem repeat detectors are published, providing heterogeneous, partly complementary, partly conflicting results.
RESULTS: We present TRAL, a tandem repeat annotation library that allows running and parsing of various detection outputs, clustering of redundant or overlapping annotations, several statistical frameworks for filtering false positive annotations, and importantly a tandem repeat annotation and refinement module based on circular profile hidden Markov models (cpHMMs). Using TRAL, we evaluated the performance of a multi-step tandem repeat annotation workflow on 547â085 sequences in UniProtKB/Swiss-Prot. The researcher can use these results to predict run-times for specific datasets, and to choose annotation complexity accordingly.
AVAILABILITY AND IMPLEMENTATION: TRAL is an open-source Python 3 library and is available, together with documentation and tutorials via http://www.vital-it.ch/software/tral.
CONTACT: [email protected]
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