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 $N_{e}\approx 10^{18}cm^{-3}$, $$, 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 kk-binomial complexity of the Thue--Morse word

Two words are $k$-binomially equivalent whenever they share the same subwords, i.e., subsequences, of length at most $k$ with the same multiplicities. This is a refinement of both abelian equivalence and the Simon congruence. The $k$-binomial complexity of an infinite word $\mathbf{x}$ maps the integer $n$ to the number of classes in the quotient, by this $k$-binomial equivalence relation, of the set of factors of length $n$ occurring in $\mathbf{x}$. This complexity measure has not been investigated very much. In this paper, we characterize the $k$-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 $k$-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 $\Psi^\ell(w)$ for an arbitrary morphism $\Psi$. 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 $\Delta(1232)$ 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 $e p \to e \gamma \pi N$ processes in terms of generalized parton distributions. We provide estimates of the contamination of the $e p \to e \gamma p$ 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

Inhibition of N-linked glycosylation impairs ALK phosphorylation and disrupts pro-survival signaling in neuroblastoma cell lines

<p>Abstract</p> <p>Background</p> <p>The Anaplastic Lymphoma Kinase (ALK) is an orphan receptor tyrosine kinase, which undergoes post-translational N-linked glycosylation. The catalytic domain of ALK was originally identified in the t(2;5) translocation that produces the unglycosylated oncogenic protein NPM-ALK, which occurs in Anaplastic Large Cell Lymphoma (ALCL). Recently, both germline and somatic activating missense mutations of ALK have been identified in neuroblastoma (NB), a pediatric cancer arising from neural crest cells. Moreover, we previously reported that ALK expression is significantly upregulated in advanced/metastatic NB. We hypothesized that ALK function may depend on N-linked glycosylation and that disruption of this post-translational modification would impair ALK activation, regardless the presence of either gene mutations or overexpression.</p> <p>Methods</p> <p>We employed tunicamycin to inhibit N-linked glycosylation. The following ALK-positive NB cell lines were used: SH-SY5Y and KELLY (ALK mutation F1174L), UKF-NB3 (ALK mutation R1275Q) and NB1 (ALK amplification). As a control, we used the NB cell lines LA1-5S and NB5 (no ALK expression), and the ALCL cell line SU-DHL1 (NPM-ALK).</p> <p>Results</p> <p>Tunicamycin treatment of ALK-positive NB cells resulted in a hypoglycosylated ALK band and in decreased amounts of mature full size receptor. Concomitantly, we observed a marked reduction of mature ALK phosphorylation. On the contrary, tunicamycin had no effects on NPM-ALK phosphorylation in SU-DHL1 cells. Moreover, phosphorylation levels of ALK downstream effectors (AKT, ERK1/2, STAT3) were clearly impaired only in ALK mutated/amplified NB cell lines, whereas no significant reduction was observed in both ALK-negative and NPM-ALK-positive cell lines. Furthermore, inhibition of N-linked glycosylation considerably impaired cell viability only of ALK mutated/amplified NB cells. Finally, the cleavage of the Poly-ADP-ribose-polymerase (PARP) suggested that apoptotic pathways may be involved in cell death.</p> <p>Conclusions</p> <p>In this study we showed that inhibition of N-linked glycosylation affects ALK phosphorylation and disrupts downstream pro-survival signaling, indicating that inhibition of this post-translational modification may be a promising therapeutic approach. However, as tunicamycin is not a likely candidate for clinical use other approaches to alter N-linked glycosylation need to be explored. Future studies will assess whether the efficacy in inhibiting ALK activity might be enhanced by the combination of ALK specific small molecule and N-linked glycosylation inhibitors.</p

Experience with model-based performance, reliability and adaptability assessment of a complex industrial architecture

In this paper, we report on our experience with the application of validated models to assess performance, reliability, and adaptability of a complex mission critical system that is being developed to dynamically monitor and control the position of an oil-drilling platform. We present real-time modeling results that show that all tasks are schedulable. We performed stochastic analysis of the distribution of task execution time as a function of the number of system interfaces. We report on the variability of task execution times for the expected system configurations. In addition, we have executed a system library for an important task inside the performance model simulator. We report on the measured algorithm convergence as a function of the number of vessel thrusters. We have also studied the system architecture adaptability by comparing the documented system architecture and the implemented source code. We report on the adaptability findings and the recommendations we were able to provide to the system’s architect. Finally, we have developed models of hardware and software reliability. We report on hardware and software reliability results based on the evaluation of the system architecture

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. BIOPLAT (1302/13).info:eu-repo/semantics/publishedVersio