113 research outputs found
From Morphology to Gene Expression Profiling in Mycosis Fungoides: Is It Still a Diagnostic Challenge?
No full textBackground: We herein review the most important clinico-pathological features of mycosis fungoides (MF). These evolving clinico-pathological aspects are paired with innovative therapeutic schemes. Moreover, we indicate cutaneous lymphomas as a new frontier of artificial intelligence application. Methods: We encompass new diagnostic and prognostic data derived from the recent medical literature describing the possible histological features which could be the targets of deep learning in conjunction with available clinical data. Results: In spite of decades of research, MF diagnosis still represents the most challenging debate from a dermatopathologist’s point of view. Genetic alterations have been identified mainly in late stages of the disease, and their importance for disease initiation is still unclear. The exploration of the genome-wide expression of individual genes in skin samples may be useful in elucidating MF pathogenesis and improving early diagnosis, while artificial intelligence could offer the possibility of searching for biomarkers of disease progression. Conclusions: MF still deserves the name of the ‘great imitator’, both clinically and histopathologically. The goal of summing up all the clinico-pathological information before reaching a final diagnosis is the approach needed to reach diagnostic accuracy, especially in early MF cases. It is advisable to think of the most common clinical presentations, to be aware of the most common histopathological features, and to interpret the results of ancillary studies only in the right clinico-pathological context
Fault prognosis for rotating electrical machines monitoring using recursive least square
No full textElectron-phonon interaction in graphite intercalation compounds
No full textMotivated by the recent discovery of superconductivity in Ca- and Yb-intercalated graphite (CaC6 and YbC6) and from the ongoing debate on the nature and role of the interlayer state in this class of compounds, in this work we critically study the electron-phonon properties of a simple model based on primitive graphite. We show that this model captures an essential feature of the electron-phonon properties of the graphite intercalation compounds, namely, the existence of a strong dormant electron-phonon interaction between interlayer and pi(*) electrons, for which we provide a simple geometrical explanation in terms of Wannier-like functions. Our findings correct the oversimplified view that nearly free-electron states cannot interact with the surrounding lattice and explain the empirical correlation between the filling of the interlayer band and the occurrence of superconductivity in graphite intercalation compounds
Internal Overview of Prostatic Cancer Cases and Quality of BRCA1 and BRCA2 NGS Data from the FFPE Tissue
No full textBackground: Comprehensive genomic profiling (CGP) has gained an important role in patients with advanced prostate cancer following the introduction of PARP inhibitors in daily clinical practice. Here, we report an overview of CGP results, specifically of BRCA1 and BRCA2 HRD-repair system genes, from patients with prostate cancer analyzed in our institution, and we compare our results with those available from more recent scientific literature. Methods: The study cohort consisted of 70 patients. Somatic DNA was extracted from Formalin-Fixed Paraffin-Embedded (FFPE) tissue using a MagCore Genomic DNA FFPE One-Step Kit for MagCore System. The DNA was quantified by EasyPGX® Real-Time qPCR and EasyPGX® Analysis Software (version 4.0.13). Tissue somatic DNA libraries were prepared with Myriapod® NGS BRCA1-2 panel-NG035 and sequenced in a Mi-Seq® System. The sequence alignment in hg19 and the variant calling were performed using Myriapod® NGS Data Analysis Software version 5.0.8 NG900-SW 5.0.8 with a software detection limit (LoD) of 95%. Variants with a coverage of 500 and VAF% ≥ 5 were evaluated. Results: Tumor tissue NGS was unsuccessful in 46/70 patients (66%). Mutations of the BRCA2 gene were detected in 4 of the samples: (1) BRCA2 ex10 c.1244A>G p.His415Arg VAF = 51.03%; (2) BRCA2 ex11 c.5946delT p.Ser1982fs VAF = 72.1%; (3) BRCA2 ex11 c.3302A>G p.His1101Arg VAF = 52.9%; and (4) BRCA2 ex11 c.3195_3198delTAAT p.Asn1066fs VAF = 51.1%. Conclusions: The results from our internal overview seem to support the data and to confirm the performance of the technical issues reported in the literature. Considering the advanced age of our patients, with 84% of men over the age of 65, the application of alternative and less invasive procedures such as liquid biopsy, could be a more suitable solution for some cases
First-principles study of excitonic effects in Raman intensities
No full textA resonance phenomenon appears in the Raman intensity when the exciting light has frequency close to electronic transitions. The theoretical prediction of the frequency-dependent Raman response of crystalline systems has received little attention. Indeed, many Raman calculations are nowadays done in the static limit (vanishing light frequency), using Density-Functional Theory and Density-Functional Perturbation Theory, thus neglecting excitonic effects. In this work [1], a finite difference method is used to obtain the frequency-dependent Raman intensity of silicon within the Many-Body Perturbation Theory (excitonic effects are included by solving the Bethe-Salpeter equation). Since the convergence with the sampling of the Brillouin Zone is extremely slow, a double-grid technique needs to be used. Two main conclusions can be drawn from our analysis. First, the double-grid technique permits to obtain well converged results without requiring huge memory and time requirements. Then, excitonic effects are of crucial importance in the resonance part of the Raman spectrum. The inclusion of these excitonic effects in the computations improves the agreement with the experimental data [2] with respect to analogous results obtained within the independent-particle approach. [1] Y. Gillet, M. Giantomassi, X. Gonze, Phys. Rev. B 88, 094305 (2013). [2] A. Compaan and H. J. Trodahl, Phys. Rev. B 29, 793 (1984)
Core electrons and self-consistency in the GW approximation from a PAW perspective
No full textDensity functional theory (DFT) performs reasonably well for the determination of structural properties of many materials, but fails to predict electronic band gap values accurately.
Such a failure of DFT is not unexpected, since there exists no formal justification for interpreting the DFT eigenvalues as addition or removal energies of the many-body system (quasiparticle energies).
An alternative approach to the study of exchange-correlation effects in many-particle systems is provided by many-body perturbation theory (MBPT), which defines a rigorous approach to description of excited-state properties based on the Green's function formalism and the concept of quasiparticle electrons. Within MBPT, one can calculate the quasiparticle (QP) energies and the QP amplitudes by approximately solving, within the so-called GW approximation, the set of coupled integro-differential equations proposed by Hedin in 1965.
The GW method generally yields significantly better values for QP energies with respect to DFT as it accounts for the dynamic many-body effects in the electron-electron interaction going beyond the mean-field approximation of independent Kohn-Sham particles. The drawback of such an involved approach, however, is its large computational cost, which is mainly due to the evaluation of dielectric matrices, their inversion, and the solution of a non-Hermitian and nonlinear eigenvalue problem.
The first part of this PhD research is devoted to the implementation of an efficient and scalable coarse-grained parallel algorithms and the development of state-of-the-art methods to solve the GW equations.
All these techniques are then applied to the study of the quasiparticle band structures of SiO2 in the alpha quartz crystalline structure. The effects of the different approximations involved in the theory, the influence of self-consistency, and a systematic analysis of the reliability of the different plasmon-pole models are presented and discussed.
The second part of this PhD work is dedicated to the implementation of a methodological approach to the solution of the GW equations based on the so-called projector augmented wave method (PAW) proposed by Blochl in 1994. This new approach permits to remove many of the limitations intrinsic to the use of the pseudopotential technique widely used for ab-initio calculations, allowing one to reach GW results closer to an all-electron implementation while still maintaining computational efficiency, and flexibility. This allows us to achieve a coherent implementation of many different algorithms which enables a detailed comparison of GW calculations not yet performed until now. Results for the quasiparticle band structure and optical spectra of prototype s- and p-compounds are discussed and compared to recent studies reported in the scientific literature (when available).(FSA 3) -- UCL, 200
Implementation of techniques for computing optical properties in 0-3 dimensions, including a real-space cutoff, in ABINIT
No full textWe have implemented the calculation of optical matrix elements with and without the inclusion of a real-space cutoff in the open-source software package ABINIT. We have also included the possibility to add the contribution arising from the non-local term of the pseudopotential operator. The implementation has been tested successfully for atoms, bulk silicon, and an oxidized silicon surface. (C) 2010 Elsevier B.V. All rights reserved
Efficient Trilinear Interpolation Technique for Bethe-Salpeter Calculations of Optical Spectra
No full textThe inclusion of excitonic effects in semiconductors with the Bethe-Salpeter equation leads to good agreement of the optical spectra with experimental measurements. However, this approach requires in general very fine meshes of wavevectors in the Brillouin Zone in order to obtain well-converged spectra, with very heavy computational load, preventing access to numerous derived quantities, as e.g. Raman intensities [1]. We present a new methodology that allows to decrease the work load to reach a given accuracy. This technique is based on a trilinear interpolation technique within the Brillouin zone, combined with the Lanczos algorithm and double-grid technique, in the spirit of Refs. [2] and [3], to achieve efficient speed-up and memory use. The technique is benchmarked in terms of accuracy on selected test cases. The scaling has also been studied from low to very-high density of points in the Brillouin Zone, showing a much better scaling than a complete Bethe-Salpeter. This approach might be used in the future for more complex calculations of optical properties. References [1] Y. Gillet, M. Giantomassi, and X. Gonze, Phys. Rev. B 88, 094305 (2013). [2] M. Rohlfing and S. G. Louie, Phys. Rev. B 62, 4927 (2000). [3] D. Kammerlander, S. Botti, M. A. L. Marques, A. Marini and C. Attaccalite, Phys. Rev. B 86, 125203 (2012)
First-Principles Study of Frequency-Dependent Resonant Raman Scattering
No full textA resonance phenomenon appears in the Raman response when the exciting light has frequency close to electronic transitions. Unlike for molecules and for graphene, the theoretical prediction of such frequency-dependent Raman response of crystalline systems has remained a challenge. Indeed, many Raman intensity first-principle calculations are nowadays done at vanishing light frequency, using static Density-Functional Perturbation Theory, thus neglecting the frequency dependence and excitonic effects. Recently, we proposed a finite-difference method for the computation of the first-order frequency-dependent Raman intensity [1], with excitonic effects described by the Bethe-Salpeter equation. We found these to be crucial for the accurate description of the experimental enhancement for laser photon energies around the gap. In this work, we generalize this approach to the more complex second-order Raman intensity, with phonon losses coming from the entire Brillouin zone. Interestingly, even without excitonic effects, one is able to capture the main relative changes in the frequency-dependent Raman spectrum at fixed laser frequencies. The excitonic effects are discussed. [1] Y. Gillet, M. Giantomassi, X. Gonze, Phys. Rev. B 88, 094305 (2013)
Novel Trilinear Interpolation Technique to Improve the Convergence Rate of Bethe-Salpeter Calculations
No full textThe inclusion of excitonic effects in semiconductors with the Bethe-Salpeter equation leads to good agreement of the optical spectra with experimental measurements. However, this approach requires in general very fine meshes of wavevectors in the Brillouin Zone in order to obtain well-converged spectra, preventing access to numerous derived quantities, as depicted e.g. in [1]. Rohlfing [2] and Kammerlander [3] have proposed different techniques to treat such fine meshes, allowing to decrease the work load to reach a given accuracy. We have designed a new methodology, based on a trilinear interpolation technique within the Brillouin zone, combined with the Lanczos algorithm, also incorporating ideas from Ref. [2,3], like a double-grid technique, to achieve superiour speed-up and memory use. We describe the implementation, and show results for selected materials. References [1] Y. Gillet, M. Giantomassi and X. Gonze, Phys. Rev. B 88, 094305 (2013) [2] M. Rohlfing and S.G. Louie, Phys. Rev. B 62, 4927 (2000) [3] D. Kammerlander, S. Botti, M.A.L. Marques, A. Marini and C. Attaccalite, Phys. Rev. B 86, 125203 (2012
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