328 research outputs found
A lower bound on CNF encodings of the at-most-one constraint
Constraint "at most one" is a basic cardinality constraint which requires
that at most one of its boolean inputs is set to . This constraint is
widely used when translating a problem into a conjunctive normal form (CNF) and
we investigate its CNF encodings suitable for this purpose. An encoding differs
from a CNF representation of a function in that it can use auxiliary variables.
We are especially interested in propagation complete encodings which have the
property that unit propagation is strong enough to enforce consistency on input
variables. We show a lower bound on the number of clauses in any propagation
complete encoding of the "at most one" constraint. The lower bound almost
matches the size of the best known encodings. We also study an important case
of 2-CNF encodings where we show a slightly better lower bound. The lower bound
holds also for a related "exactly one" constraint.Comment: 38 pages, version 3 is significantly reorganized in order to improve
readabilit
Diagnosing and measuring incompatibilities between pairs of services
International audienceThis text presents a tool, from its design to its implementation, which detects all behavioural incompatibilities between two service interfaces. Unlike prior work, the proposed solution does not simply check whether two services are incompatible or not, it rather provides detailed diagnosis, including the incompatibilities and for each one the location in the service interfaces where these incompatibilities occur. A measure of similarity between interfaces which considers outputs from the detection algorithm is proposed too. A visual report of the comparison analysis is also provided which pinpoints a set of incompatibilities that cause a behavioural interface not to simulate another one
Tau Be or not Tau Be? - A Perspective on Service Compatibility and Substitutability
One of the main open research issues in Service Oriented Computing is to
propose automated techniques to analyse service interfaces. A first problem,
called compatibility, aims at determining whether a set of services (two in
this paper) can be composed together and interact with each other as expected.
Another related problem is to check the substitutability of one service with
another. These problems are especially difficult when behavioural descriptions
(i.e., message calls and their ordering) are taken into account in service
interfaces. Interfaces should capture as faithfully as possible the service
behaviour to make their automated analysis possible while not exhibiting
implementation details. In this position paper, we choose Labelled Transition
Systems to specify the behavioural part of service interfaces. In particular,
we show that internal behaviours (tau transitions) are necessary in these
transition systems in order to detect subtle errors that may occur when
composing a set of services together. We also show that tau transitions should
be handled differently in the compatibility and substitutability problem: the
former problem requires to check if the compatibility is preserved every time a
tau transition is traversed in one interface, whereas the latter requires a
precise analysis of tau branchings in order to make the substitution preserve
the properties (e.g., a compatibility notion) which were ensured before
replacement.Comment: In Proceedings WCSI 2010, arXiv:1010.233
A PCR-mutagenesis strategy for rapid detection of mutations in codon 634 of the ret proto-oncogene related to MEN 2A.
BACKGROUND: Multiple endocrine neoplasias type 2A (MEN 2A) is a dominantly inherited cancer syndrome. Missence mutations in the codon encoding cysteine 634 of the ret proto-oncogene have been found in 85% of the MEN 2A families. The main tumour type always present in MEN 2A is medullar thyroid carcinoma (MTC). Only 25% of all MTC are hereditary, and generally they are identified by a careful family history. However, some familial MTCs are not easily detected by this means and underdiagnosis of MEN 2A is suspected. METHODS: DNA samples from MEN 2A patients were amplified by PCR. The products were incubated with the restriction enzyme Bst ApI or Bgl I. The samples were loaded in non-denaturing 10% Polyacrilamyde Gel and run at 120 volts for 40 min. The gels were stained with 10 μg/ml ethidium bromide, and the bands were visualized under a UV lamp. RESULTS: We developed a PCR-mutagenic method to check the integrity of the three bases of the cysteine 634 codon. CONCLUSION: The method can be used to detect inherited mutations in MTC patients without a clear family history. The method is relatively simple to use as a routine test in these patients to decrease the underdiagnosis of MEN 2A. In addition, the assay can be used to screen affected families with any mutation in cysteine 634
DOSCATs: Double standards for protein quantification
The two most common techniques for absolute protein quantification are based on either mass spectrometry (MS) or on immunochemical techniques, such as western blotting (WB). Western blotting is most often used for protein identification or relative quantification, but can also be deployed for absolute quantification if appropriate calibration standards are used. MS based techniques offer superior data quality and reproducibility, but WB offers greater sensitivity and accessibility to most researchers. It would be advantageous to apply both techniques for orthogonal quantification, but workflows rarely overlap. We describe DOSCATs (DOuble Standard conCATamers), novel calibration standards based on QconCAT technology, to unite these platforms. DOSCATs combine a series of epitope sequences concatenated with tryptic peptides in a single artificial protein to create internal tryptic peptide standards for MS as well as an intact protein bearing multiple linear epitopes. A DOSCAT protein was designed and constructed to quantify five proteins of the NF-κB pathway. For three target proteins, protein fold change and absolute copy per cell values measured by MS and WB were in excellent agreement. This demonstrates that DOSCATs can be used as multiplexed, dual purpose standards, readily deployed in a single workflow, supporting seamless quantitative transition from MS to WB
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Conifer DBMagic: a database housing multiple de novo transcriptome assemblies for 12 diverse conifer species
Conifers comprise an ancient and widespread plant lineage of enormous commercial and ecological value. However, compared to model woody angiosperms, such as Populus and Eucalyptus, our understanding of conifers remains quite limited at a genomic level. Large genome sizes (10,000–40,000 Mbp) and large amounts of repetitive DNA have limited efforts to produce a conifer reference genome, and genomic resource development has focused primarily on characterization of expressed sequences. Here, we report the completion of a conifer transcriptome sequencing project undertaken in collaboration with the U.S. DOE Joint Genome Institute that resulted in production of almost 12 million sequence reads. Five loblolly pine (Pinus taeda) cDNA libraries representing multiple tissues, treatments, and genotypes produced over four million sequence reads that, along with available Sanger expressed sequence tags, were used to create contig assemblies using three different assembly algorithms: Newbler, MiraEST, and NGen. In addition, libraries from 11 other conifer species, as well as one member of the Gnetales (Gnetum gnemon), produced 0.4 to 1.2 million sequence reads each. Among the selected conifer species were representatives of each of the seven phylogenetic families in the Coniferales: Araucariaceae, Cephalotaxaceae, Cupressaceae, Pinaceae, Podocarpaceae, Sciadopityaceae, and Taxaceae. Transcriptome builds for each species were generated using each of the three assemblers. All contigs for every species generated using each assembler can be obtained from Conifer DBMagic, a public database for searching, viewing, and downloading contig sequences, the associated sequence reads, and their annotations.Keywords: Database,
Gene models,
Pinus,
Comparative phylogenomics,
Annotation,
Transcriptome,
Coniferale
Constraint solving in uncertain and dynamic environments - a survey
International audienceThis article follows a tutorial, given by the authors on dynamic constraint solving at CP 2003 (Ninth International Conference on Principles and Practice of Constraint Programming) in Kinsale, Ireland. It aims at offering an overview of the main approaches and techniques that have been proposed in the domain of constraint satisfaction to deal with uncertain and dynamic environments
Subcellular peptide localization in single identified neurons by capillary microsampling mass spectrometry
Single cell mass spectrometry (MS) is uniquely positioned for the sequencing and identification of peptides in rare cells. Small peptides can take on different roles in subcellular compartments. Whereas some peptides serve as neurotransmitters in the cytoplasm, they can also function as transcription factors in the nucleus. Thus, there is a need to analyze the subcellular peptide compositions in identified single cells. Here, we apply capillary microsampling MS with ion mobility separation for the sequencing of peptides in single neurons of the mollusk Lymnaea stagnalis, and the analysis of peptide distributions between the cytoplasm and nucleus of identified single neurons that are known to express cardioactive Phe-Met-Arg-Phe amide-like (FMRFamide-like) neuropeptides. Nuclei and cytoplasm of Type 1 and Type 2 F group (Fgp) neurons were analyzed for neuropeptides cleaved from the protein precursors encoded by alternative splicing products of the FMRFamide gene. Relative abundances of nine neuropeptides were determined in the cytoplasm. The nuclei contained six of these peptides at different abundances. Enabled by its relative enrichment in Fgp neurons, a new 28-residue neuropeptide was sequenced by tandem MS
Principles for developing and adapting clinical practice guidelines and guidance for pandemics, wars, shortages, and other crises and emergencies: the PAGE criteria
Development of international clinical practice guidelines: benefits, limitations, and alternative forms of international collaboration
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