Negative Subtraction Hybridization: An efficient method to isolate large numbers of condition-specific cDNAs

BACKGROUND: The construction of cDNA libraries is a useful tool to understand gene expression in organisms under different conditions, but random sequencing of unbiased cDNA collections is laborious and can give rise to redundant EST collections. We aimed to isolate cDNAs of messages induced by switching Aspergillus nidulans from growth on glucose to growth on selected polysaccharides. Approximately 4,700 contigs from 12,320 ESTs were already available from a cDNA library representing transcripts isolated from glucose-grown A. nidulans during asexual development. Our goals were to expand the cDNA collection without repeated sequencing of previously identified ESTs and to find as many transcripts as possible that are specifically induced in complex polysaccharide metabolism. RESULTS: We have devised a Negative Subtraction Hybridization (NSH) method and tested it in A. nidulans. NSH entails screening a plasmid library made from cDNAs prepared from cells grown under a selected physiological condition with labeled cDNA probes prepared from another physiological condition. Plasmids with inserts that failed to hybridize to cDNA probes through two rounds of screening (i.e. negatives) indicate that they are transcripts present at low concentration in the labeled probe pool. Thus, these transcripts will be predominantly condition-specific, along with some rare transcripts. In a screen for transcripts induced by switching the carbon source from glucose to 12 selected polysaccharides, 3,532 negatives were isolated from approximately 100,000 surveyed colonies using this method. Negative clones were end-sequenced and assembled into 2,039 contigs, of which 1,722 were not present in the previously characterized glucose-grown cDNA library. Single-channel microarray hybridization experiments confirmed that the majority of the negatives represented genes that were differentially induced by a switch from growth in glucose to one or more of the polysaccharides. CONCLUSIONS: The Negative Subtraction Hybridization method described here has several practical benefits. This method can be used to screen any existing cDNA library, including full-length and pooled libraries, and does not rely on PCR or sequence information. In addition, NSH is a cost-effective method for the isolation of novel, full-length cDNAs for differentially expressed transcripts or enrichment of rare transcripts

Statistical relational learning with soft quantifiers

Quantification in statistical relational learning (SRL) is either existential or universal, however humans might be more inclined to express knowledge using soft quantifiers, such as ``most'' and ``a few''. In this paper, we define the syntax and semantics of PSL^Q, a new SRL framework that supports reasoning with soft quantifiers, and present its most probable explanation (MPE) inference algorithm. To the best of our knowledge, PSL^Q is the first SRL framework that combines soft quantifiers with first-order logic rules for modelling uncertain relational data. Our experimental results for link prediction in social trust networks demonstrate that the use of soft quantifiers not only allows for a natural and intuitive formulation of domain knowledge, but also improves the accuracy of inferred results

Two-color interferometer for the study of laser filamentation triggered electric discharges in air

International audienceWe present a space and time resolved interferometric plasma diagnostic for use on plasmas where neutral-bound electron contribution to the refractive index cannot be neglected. By recording simultaneously the plasma optical index at 532 and 1064 nm, we are able to extract independently the neutral and free electron density profiles. We report a phase resolution of 30 mrad, corresponding to a maximum resolution on the order of 4 × 10 22 m −3 for the electron density, and of 10 24 m −3 for the neutral density. The interferometer is demonstrated on centimeter-scale sparks triggered by laser filamentation in air with typical currents of a few tens of A

Greenhouse gas emissions of bio-based diapers containing chemically modified protein superabsorbents

Replacing the current mainly fossil-based, disposable, and non-biodegradable sanitary products with sustainable, functional alternatives is an industry priority. Suggested biobased alternatives require evaluation of their actual impact on greenhouse gas (GHG) emissions. We evaluated GHG emissions of biobased baby diapers as the most consumed sanitary product, using a biodegradable functionalized protein superabsorbent polymer (bioSAP) and compared them with currently used fossil-based counterparts. Assessment of the diapers also included estimated GHG emissions from the production of the biobased components, transport, and end-of-life combustion of these items. It was shown that only a few of the biobased diaper alternatives resulted in lower GHG emissions than commercial diapers containing fossil-based materials. At the same time, it was demonstrated that the production of the bioSAP via chemical modification of a protein raw material is the primary GHG contributor, with 78% of the total emissions. Reduction of the GHG contribution of the bioSAP production was achieved via a proposed recycling route of the functionalization agent, reducing the GHG emissions by 13% than if no recycling was carried out. Overall, we demonstrated that reduced and competitive GHG emissions could be achieved in sanitary articles using biobased materials, thereby contributing to a sanitary industry producing disposable products with less environmental pollution while allowing customers to keep their current consumption patterns

Forward THz radiation emission by femtosecond filamentation in gases: theory and experiment

International audienceA transition–Cherenkov electromagnetic emission by a femtosecond laser pulse propagating in a self-induced plasma channel in air has been very recently proposed as mechanism for production of terahertz (THz) radiation in the forward direction. In this paper, we study in detail the theory of the transition–Cherenkov process. The theoretical model is developed and compared with recent experimental results for several gases

Theory for the coupling between longitudinal phonons and intrinsic Josephson oscillations in layered superconductors

In this publication a microscopic theory for the coupling of intrinsic Josephson oscillations in layered superconductors with longitudinal c-axis-phonons is developed. It is shown that the influence of lattice vibrations on the c-axis transport can be fully described by introducing an effective longitudinal dielectric function. Resonances in the I-V-characteristic appear at van Hove singularities of both acoustical and optical longitudinal phonon branches. This provides a natural explanation of the recently discovered subgap structures in the I-V-characteristic of highly anisotropic cuprate superconductors. The effect of the phonon dispersion on the damping of these resonances and the coupling of Josephson oscillations in different resistive junctions due to phonons are discussed in detail.Comment: submitted to Phys. Rev. B, corrections following referee repor

On the Informational Comparison of Qualitative Fuzzy Measures

International audienceFuzzy measures or capacities are the most general representation of uncertainty functions. However, this general class has been little explored from the point of view of its information content, when degrees of uncertainty are not supposed to be numerical, and belong to a finite qualitative scale, except in the case of possibility or necessity measures. The thrust of the paper is to define an ordering relation on the set of qualitative capacities expressing the idea that one is more informative than another, in agreement with the possibilistic notion of relative specificity. To this aim, we show that the class of qualitative capacities can be partitioned into equivalence classes of functions containing the same amount of information. They only differ by the underlying epistemic attitude such as pessimism or optimism. A meaningful information ordering between capacities can be defined on the basis of the most pessimistic (resp. optimistic) representatives of their equivalence classes. It is shown that, while qualitative capacities bear strong similarities to belief functions, such an analogy can be misleading when it comes to information content

General relativistic corrections to the Sagnac effect

The difference in travel time of corotating and counter-rotating light waves in the field of a central massive and spinning body is studied. The corrections to the special relativistic formula are worked out in a Kerr field. Estimation of numeric values for the Earth and satellites in orbit around it show that a direct measurement is in the order of concrete possibilities.Comment: REVTex, accepted for publication on Phys. Rev.

From Analogical Proportion to Logical Proportions

International audienceGiven a 4-tuple of Boolean variables (a, b, c, d), logical proportions are modeled by a pair of equivalences relating similarity indicators ( a∧b and a¯∧b¯), or dissimilarity indicators ( a∧b¯ and a¯∧b) pertaining to the pair (a, b), to the ones associated with the pair (c, d). There are 120 semantically distinct logical proportions. One of them models the analogical proportion which corresponds to a statement of the form “a is to b as c is to d”. The paper inventories the whole set of logical proportions by dividing it into five subfamilies according to what they express, and then identifies the proportions that satisfy noticeable properties such as full identity (the pair of equivalences defining the proportion hold as true for the 4-tuple (a, a, a, a)), symmetry (if the proportion holds for (a, b, c, d), it also holds for (c, d, a, b)), or code independency (if the proportion holds for (a, b, c, d), it also holds for their negations (a¯,b¯,c¯,d¯)). It appears that only four proportions (including analogical proportion) are homogeneous in the sense that they use only one type of indicator (either similarity or dissimilarity) in their definition. Due to their specific patterns, they have a particular cognitive appeal, and as such are studied in greater details. Finally, the paper provides a discussion of the other existing works on analogical proportions