222 research outputs found
Suffix conjugates for a class of morphic subshifts
Let A be a finite alphabet and f: A^* --> A^* be a morphism with an iterative
fixed point f^\omega(\alpha), where \alpha{} is in A. Consider the subshift (X,
T), where X is the shift orbit closure of f^\omega(\alpha) and T: X --> X is
the shift map. Let S be a finite alphabet that is in bijective correspondence
via a mapping c with the set of nonempty suffixes of the images f(a) for a in
A. Let calS be a subset S^N be the set of infinite words s = (s_n)_{n\geq 0}
such that \pi(s):= c(s_0)f(c(s_1)) f^2(c(s_2))... is in X. We show that if f is
primitive and f(A) is a suffix code, then there exists a mapping H: calS -->
calS such that (calS, H) is a topological dynamical system and \pi: (calS, H)
--> (X, T) is a conjugacy; we call (calS, H) the suffix conjugate of (X, T). In
the special case when f is the Fibonacci or the Thue-Morse morphism, we show
that the subshift (calS, T) is sofic, that is, the language of calS is regular
Slow and fast micro-field components in warm and dense hydrogen plasmas
The aim of this work is the investigation of the statistical properties of
local electric fields in an ion-electron two component plasmas for coupled
conditions. The stochastic fields at a charged or at a neutral point in plasmas
involve both slow and fast fluctuation characteristics. The statistical study
of these local fields based on a direct time average is done for the first
time. For warm and dense plasma conditions, typically , , well controlled molecular dynamics (MD)
simulations of neutral hydrogen, protons and electrons have been carried out.
Relying on these \textit{ab initio} MD calculations this work focuses on an
analysis of the concepts of statistically independent slow and fast local field
components, based on the consideration of a time averaged electric field. Large
differences are found between the results of these MD simulations and
corresponding standard results based on static screened fields. The effects
discussed are of importance for physical phenomena connected with stochastic
electric field fluctuations, e.g., for spectral line broadening in dense
plasmas.Comment: 4 pages, 4 figures, submitted to Phys. Rev. Let
Enumeration and Decidable Properties of Automatic Sequences
We show that various aspects of k-automatic sequences -- such as having an
unbordered factor of length n -- are both decidable and effectively enumerable.
As a consequence it follows that many related sequences are either k-automatic
or k-regular. These include many sequences previously studied in the
literature, such as the recurrence function, the appearance function, and the
repetitivity index. We also give some new characterizations of the class of
k-regular sequences. Many results extend to other sequences defined in terms of
Pisot numeration systems
Computing the -binomial complexity of the Thue--Morse word
Two words are -binomially equivalent whenever they share the same
subwords, i.e., subsequences, of length at most with the same
multiplicities. This is a refinement of both abelian equivalence and the Simon
congruence. The -binomial complexity of an infinite word maps
the integer to the number of classes in the quotient, by this -binomial
equivalence relation, of the set of factors of length occurring in
. This complexity measure has not been investigated very much. In
this paper, we characterize the -binomial complexity of the Thue--Morse
word. The result is striking, compared to more familiar complexity functions.
Although the Thue--Morse word is aperiodic, its -binomial complexity
eventually takes only two values. In this paper, we first obtain general
results about the number of occurrences of subwords appearing in iterates of
the form for an arbitrary morphism . We also thoroughly
describe the factors of the Thue--Morse word by introducing a relevant new
equivalence relation
Pion production in deeply virtual Compton scattering
Using a soft pion theorem based on chiral symmetry and a
resonance model we propose an estimate for the production cross section of low
energy pions in the deeply virtual Compton scattering (DVCS) process. In
particular, we express the processes in terms of
generalized parton distributions. We provide estimates of the contamination of
the DVCS observables due to this associated pion
production processes when the experimental data are not fully exclusive, for a
set of kinematical conditions representative of present or planned experiments
at JLab, HERMES and COMPASS.Comment: 50 pages, 22 figure
Periodic points in random substitution subshifts
We study various aspects of periodic points for random substitution subshifts. In order to do so, we introduce a new property for random substitutions called the disjoint images condition. We provide a procedure for determining the property for compatible random substitutions—random substitutions for which a well-defined abelianisation exists. We find some simple necessary criteria for primitive, compatible random substitutions to admit periodic points in their subshifts. In the case that the random substitution further has disjoint images and is of constant length, we provide a stronger criterion. A method is outlined for enumerating periodic points of any specified length in a random substitution subshift
Detection of ALK fusion transcripts in FFPE lung cancer samples by NanoString technology
Background: ALK-rearranged lung cancers exhibit specific pathologic and clinical features and are responsive to anti-ALK therapies. Therefore, the detection of ALK-rearrangement is fundamental for personalized lung cancer therapy. Recently, new molecular techniques, such as NanoString nCounter, have been developed to detect ALK fusions with more accuracy and sensitivity.
Methods: In the present study, we intended to validate a NanoString nCounter ALK-fusion panel in routine biopsies of FFPE lung cancer patients. A total of 43 samples were analyzed, 13 ALK-positive and 30 ALK-negative, as previously detected by FISH and/or immunohistochemistry.
Results: The NanoString panel detected the presence of the EML4-ALK, KIF5B-ALK and TFG-ALK fusion variants. We observed that all the 13 ALK-positive cases exhibited genetic aberrations by the NanoString methodology. Namely, six cases (46.15%) presented EML-ALK variant 1, two (15.38%) presented EML-ALK variant 2, two (15.38%) presented EML-ALK variant 3a, and three (23.07%) exhibited no variant but presented unbalanced expression between 5'/3' exons, similar to other positive samples. Importantly, for all these analyses, the initial input of RNA was 100 ng, and some cases displayed poor RNA quality measurements.
Conclusions: In this study, we reported the great utility of NanoString technology in the assessment of ALK fusions in routine lung biopsies of FFPE specimens.This study was partially funded by FINEP (MCTI/FINEP/MS/SCTIE/DECIT), Brazil.
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