DaMiRseq—an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification

Abstract Summary RNA-Seq is becoming the technique of choice for high-throughput transcriptome profiling, which, besides class comparison for differential expression, promises to be an effective and powerful tool for biomarker discovery. However, a systematic analysis of high-dimensional genomic data is a demanding task for such a purpose. DaMiRseq offers an organized, flexible and convenient framework to remove noise and bias, select the most informative features and perform accurate classification. Availability and implementation DaMiRseq is developed for the R environment (R ≥ 3.4) and is released under GPL (≥2) License. The package runs on Windows, Linux and Macintosh operating systems and is freely available to non-commercial users at the Bioconductor open-source, open-development software project repository (https://bioconductor.org/packages/DaMiRseq/). In compliance with Bioconductor standards, the authors ensure stable package maintenance through software and documentation updates. Supplementary information Supplementary data are available at Bioinformatics online

Towards joint reconstruction of noise and losses in quantum channels

The calibration of a quantum channel, i.e. the determination of the transmission losses affecting it, is definitely one of the principal objectives in both the quantum communication and quantum metrology frameworks. Another task of the utmost relevance is the identification, e.g. by extracting its photon number distribution, of the noise potentially present in the channel. Here we present a protocol, based on the response of a photon-number-resolving detector at different quantum efficiencies, able to accomplish both of these tasks at once, providing with a single measurement an estimate of the transmission losses as well as the photon statistics of the noise present in the exploited quantum channel. We show and discuss the experimental results obtained in the practical implementation of such protocol, with different kinds and levels of noise.Comment: 6 pages, 4 figure

Positive Operator-Valued Measure reconstruction of a beam-splitter tree based photon-number-resolving detector

Here we present a reconstruction of the Positive Operator-Value Measurement of a photon-number-resolving detector comprised of three 50:50 beamsplitters in a tree configuration, terminated with four single-photon avalanche detectors. The four detectors' outputs are processed by an electronic board that discriminates detected photon number states from 0 to 4 and implements a "smart counting" routine to compensate for dead time issues at high count rates

Quantal Two-Centre Coulomb Problem treated by means of the Phase-Integral Method II. Quantization Conditions in the Symmetric Case Expressed in Terms of Complete Elliptic Integrals. Numerical Illustration

The contour integrals, occurring in the arbitrary-order phase-integral quantization conditions given in a previous paper, are in the first- and third-order approximations expressed in terms of complete elliptic integrals in the case that the charges of the Coulomb centres are equal. The evaluation of the integrals is facilitated by the knowledge of quasiclassical dynamics. The resulting quantization conditions involving complete elliptic integrals are solved numerically to obtain the energy eigenvalues and the separation constants of the $1s\sigma$ and $2p\sigma$ states of the hydrogen molecule ion for various values of the internuclear distance. The accuracy of the formulas obtained is illustrated by comparison with available numerically exact results.Comment: 19 pages, RevTeX 4, 4 EPS figures, submitted to J. Math. Phy

Quantum and classical characterization of single/few photon detectors

This paper's purpose is to review the results recently obtained in the Quantum Optics labs of the National Institute of Metrological Research (INRIM) in the field of single- and few-photon detectors calibration, from both the classical and quantum viewpoint. In the first part of the paper is presented the calibration of a single-photon detector with absolute methods, while in the second part we focus on photon-number-resolving detectors, discussing both the classical and quantum characterization of such devices.Comment: Quantum Matter in pres

Experiment Investigating the Connection between Weak Values and Contextuality

Weak value measurements have recently given rise to a large interest for both the possibility of measurement amplification and the chance of further quantum mechanics foundations investigation. In particular, a question emerged about weak values being proof of the incompatibility between Quantum Mechanics and Non-Contextual Hidden Variables Theories (NCHVT). A test to provide a conclusive answer to this question was given in [M. Pusey, Phys. Rev. Lett. 113, 200401 (2014)], where a theorem was derived showing the NCHVT incompatibility with the observation of anomalous weak values under specific conditions. In this paper we realize this proposal, clearly pointing out the strict connection between weak values and the contextual nature of Quantum Mechanics.Comment: 5 pages, 4 figure

Carcinoid Crisis: A Misunderstood and Unrecognized Oncological Emergency

Carcinoid Crisis represents a rare and extremely dangerous manifestation that can occur in patients with Neuroendocrine Tumors (NETs). It is characterized by a sudden onset of hemodynamic instability, sometimes associated with the classical symptoms of carcinoid syndrome, such as bronchospasm and flushing. Carcinoid Crisis seems to be caused by a massive release of vasoactive substances, typically produced by neuroendocrine cells, and can emerge after abdominal procedures, but also spontaneously in rare instances. To date, there are no empirically derived guidelines for the management of this cancer-related medical emergency, and the available evidence essentially comes from single-case reports or dated small retrospective series. A transfer to the Intensive Care Unit may be necessary during the acute setting, when the severe hypotension becomes unresponsive to standard practices, such as volemic filling and the infusion of vasopressor therapy. The only effective strategy is represented by prevention. The administration of octreotide, anxiolytic and antihistaminic agents represents the current treatment approach to avoid hormone release and prevent major complications. However, no standard protocols are available, resulting in great variability in terms of schedules, doses, ways of administration and timing of prophylactic treatments

An extremely low-noise heralded single-photon source: a breakthrough for quantum technologies

Low noise single-photon sources are a critical element for quantum technologies. We present a heralded single-photon source with an extremely low level of residual background photons, by implementing low-jitter detectors and electronics and a fast custom-made pulse generator controlling an optical shutter (a LiNbO3 waveguide optical switch) on the output of the source. This source has a second-order autocorrelation g^{(2)}(0)=0.005(7), and an "Output Noise Factor" (defined as the ratio of the number of noise photons to total photons at the source output channel) of 0.25(1)%. These are the best performance characteristics reported to date

Gene expression profiling reveals novel protective effects of Aminaphtone on ECV304 endothelial cells

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