7,130 research outputs found
Physics-based analysis of Affymetrix microarray data
We analyze publicly available data on Affymetrix microarrays spike-in
experiments on the human HGU133 chipset in which sequences are added in
solution at known concentrations. The spike-in set contains sequences of
bacterial, human and artificial origin. Our analysis is based on a recently
introduced molecular-based model [E. Carlon and T. Heim, Physica A 362, 433
(2006)] which takes into account both probe-target hybridization and
target-target partial hybridization in solution. The hybridization free
energies are obtained from the nearest-neighbor model with experimentally
determined parameters. The molecular-based model suggests a rescaling that
should result in a "collapse" of the data at different concentrations into a
single universal curve. We indeed find such a collapse, with the same
parameters as obtained before for the older HGU95 chip set. The quality of the
collapse varies according to the probe set considered. Artificial sequences,
chosen by Affymetrix to be as different as possible from any other human genome
sequence, generally show a much better collapse and thus a better agreement
with the model than all other sequences. This suggests that the observed
deviations from the predicted collapse are related to the choice of probes or
have a biological origin, rather than being a problem with the proposed model.Comment: 11 pages, 10 figure
Dynamics of the Pionium with the Density Matrix Formalism
The evolution of pionium, the hydrogen-like atom, while passing
through matter is solved within the density matrix formalism in the first Born
approximation. We compare the influence on the pionium break-up probability
between the standard probabilistic calculations and the more precise picture of
the density matrix formalism accounting for interference effects. We focus our
general result in the particular conditions of the DIRAC experiment at CERN.Comment: 14 pages, 2 figures, submitted to J. Phys. B: At. Mol. Phy
Investigating the timecourse of accessing conversational implicatures during incremental sentence interpretation
Many contextual inferences in utterance interpretation are explained as following from the nature of conversation and the assumption that participants are rational. Recent psycholinguistic research has focussed on certain of these ‘Gricean’ inferences and have revealed that comprehenders can access them in online interpretation. However there have been mixed results as to the time-course of access. Some results show that Gricean inferences can be accessed very rapidly, as rapidly as any other contextually specified information (Sedivy, 2003; Grodner, Klein, Carbery, & Tanenhaus, 2010); while other studies looking at the same kind of inference suggest that access to Gricean inferences are delayed relative to other aspects of semantic interpretation (Huang & Snedeker, 2009; in press). While previous timecourse research has focussed on Gricean inferences that support the online assignment of reference to definite expressions, the study reported here examines the timecourse of access to scalar implicatures, which enrich the meaning of an utterance beyond the semantic interpretation. Even if access to Gricean inference in support of reference assignment may be rapid, it is still unknown whether genuinely enriching scalar implicatures are delayed. Our results indicate that scalar implicatures are accessed as rapidly as other contextual inferences. The implications of our results are discussed in reference to the architecture of language comprehension
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