Dissect: detection and characterization of novel structural alterations in transcribed sequences

Motivation: Computational identification of genomic structural variants via high-throughput sequencing is an important problem for which a number of highly sophisticated solutions have been recently developed. With the advent of high-throughput transcriptome sequencing (RNA-Seq), the problem of identifying structural alterations in the transcriptome is now attracting significant attention

On the evolution of superposition of squeezed displaced number states with the multiphoton Jaynes-Cummings model

In this paper we discuss the quantum properties for superposition of squeezed displaced number states against multiphoton Jaynes-Cummings model (JCM). In particular, we investigate atomic inversion, photon-number distribution, purity, quadrature squeezing, Mandel $Q$ parameter and Wigner function. We show that the quadrature squeezing for three-photon absorption case can exhibit revivals and collapses typical to those occurring in the atomic inversion for one-photon absorption case. Also we prove that for odd number absorption parameter there is a connection between the evolution of the atomic inversion and the evolution of the Wigner function at the origin in phase space. Furthermore, we show that the nonclassical states whose the Wigner functions values at the origins are negative will be always nonclassical when they are evolving through the JCM with even absorption parameter. Also we demonstrate that various types of cat states can be generated via this system.Comment: 27 pages, 10 figure

Barut-Girardello coherent states for u(p,q) and sp(N,R) and their macroscopic superpositions

The Barut-Girardello coherent states (BG CS) representation is extended to the noncompact algebras u(p,q) and sp(N,R) in (reducible) quadratic boson realizations. The sp(N,R) BG CS take the form of multimode ordinary Schr\"odinger cat states. Macroscopic superpositions of 2^{n-1} sp(N,R) CS (2^n canonical CS, n=1,2,...) are pointed out which are overcomplete in the N-mode Hilbert space and the relation between the canonical CS and the u(p,q) BG-type CS representations is established. The sets of u(p,q) and sp(N,R) BG CS and their discrete superpositions contain many states studied in quantum optics (even and odd N-mode CS, pair CS) and provide an approach to quadrature squeezing, alternative to that of intelligent states. New subsets of weakly and strongly nonclassical states are pointed out and their statistical properties (first- and second-order squeezing, photon number distributions) are discussed. For specific values of the angle parameters and small amplitude of the canonical CS components these states approaches multimode Fock states with one, two or three bosons/photons. It is shown that eigenstates of a squared non-Hermitian operator A^2 (generalized cat states) can exhibit squeezing of the quadratures of A.Comment: 29 pages, LaTex, 5 figures. Improvements in text, corrections in some formulas. To appear in J. Phys. A, v. 3

Robustness of massively parallel sequencing platforms

The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications. © 2015 Kavak et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Robertson Intelligent States

Diagonalization of uncertainty matrix and minimization of Robertson inequality for n observables are considered. It is proved that for even n this relation is minimized in states which are eigenstates of n/2 independent complex linear combinations of the observables. In case of canonical observables this eigenvalue condition is also necessary. Such minimizing states are called Robertson intelligent states (RIS). The group related coherent states (CS) with maximal symmetry (for semisimple Lie groups) are particular case of RIS for the quadratures of Weyl generators. Explicit constructions of RIS are considered for operators of su(1,1), su(2), h_N and sp(N,R) algebras. Unlike the group related CS, RIS can exhibit strong squeezing of group generators. Multimode squared amplitude squeezed states are naturally introduced as sp(N,R) RIS. It is shown that the uncertainty matrices for quadratures of q-deformed boson operators a_{q,j} (q > 0) and of any k power of a_j = a_{1,j} are positive definite and can be diagonalized by symplectic linear transformations. PACS numbers: 03.65.Fd, 42.50.DvComment: 23 pages, LaTex. Minor changes in text and references. Accepted in J. Phys.

Siponimod vs placebo in active secondary progressive multiple sclerosis: a post hoc analysis from the phase 3 EXPAND study.

BACKGROUND Siponimod is a sphingosine 1-phosphate receptor modulator approved for active secondary progressive multiple sclerosis (aSPMS) in most countries; however, phase 3 EXPAND study data are from an SPMS population with/without disease activity. A need exists to characterize efficacy/safety of siponimod in aSPMS. METHODS Post hoc analysis of participants with aSPMS (≥ 1 relapse in 2 years before study and/or ≥ 1 T1 gadolinium-enhancing [Gd +] magnetic resonance imaging [MRI] lesions at baseline) receiving oral siponimod (2 mg/day) or placebo for up to 3 years in EXPAND. ENDPOINTS 3-month/6-month confirmed disability progression (3mCDP/6mCDP); 3-month confirmed ≥ 20% worsening in Timed 25-Foot Walk (T25FW); 6-month confirmed improvement/worsening in Symbol Digit Modalities Test (SDMT) scores (≥ 4-point change); T2 lesion volume (T2LV) change from baseline; number of T1 Gd + lesions baseline-month 24; number of new/enlarging (N/E) T2 lesions over all visits. RESULTS Data from 779 participants with aSPMS were analysed. Siponimod reduced risk of 3mCDP/6mCDP vs placebo (by 31%/37%, respectively; p < 0.01); there was no significant effect on T25FW. Siponimod increased likelihood of 6-month confirmed SDMT improvement vs placebo (by 62%; p = 0.007) and reduced risk of 6-month confirmed SDMT worsening (by 27%; p = 0.060). Siponimod was associated with less increase in T2LV (1316.3 vs 13.3 mm3; p < 0.0001), and fewer T1 Gd + and N/E T2 lesions than placebo (85% and 80% reductions, respectively; p < 0.0001). CONCLUSIONS In aSPMS, siponimod reduced risk of disability progression and was associated with benefits on cognition and MRI outcomes vs placebo. TRIAL REGISTRATION ClinicalTrials.gov number: NCT01665144

A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data

Motivation: Copy Number Variants (CNVs) are important genetic factors for studying human diseases. While high-throughput whole genome re-sequencing provides multiple lines of evidence for detecting CNVs, computational algorithms need to be tailored for different type or size of CNVs under different experimental designs. Results: To achieve optimal power and resolution of detecting CNVs at low depth of coverage, we implemented a Hidden Markov Model that integrates both depth of coverage and mate-pair relationship. The novelty of our algorithm is that we infer the likelihood of carrying a deletion jointly from multiple mate pairs in a region without the requirement of a single mate pairs being obvious outliers. By integrating all useful information in a comprehensive model, our method is able to detect medium-size deletions (200-2000bp) at low depth (<10× per sample). We applied the method to simulated data and demonstrate the power of detecting medium-size deletions is close to theoretical values. Availability: A program implemented in Java, Zinfandel, is available at http://www.cs.columbia.edu/~itsik/zinfandel

Superhard Phases of Simple Substances and Binary Compounds of the B-C-N-O System: from Diamond to the Latest Results (a Review)

The basic known and hypothetic one- and two-element phases of the B-C-N-O system (both superhard phases having diamond and boron structures and precursors to synthesize them) are described. The attention has been given to the structure, basic mechanical properties, and methods to identify and characterize the materials. For some phases that have been recently described in the literature the synthesis conditions at high pressures and temperatures are indicated.Comment: Review on superhard B-C-N-O phase

Assessing the Potential Impacts to Riparian Ecosystems Resulting from Hemlock Mortality in Great Smoky Mountains National Park

Hemlock Woolly Adelgid (Adelges tsugae) is spreading across forests in eastern North America, causing mortality of eastern hemlock (Tsuga canadensis [L.] Carr.) and Carolina hemlock (Tsuga caroliniana Engelm.). The loss of hemlock from riparian forests in Great Smoky Mountains National Park (GSMNP) may result in significant physical, chemical, and biological alterations to stream environments. To assess the influence of riparian hemlock stands on stream conditions and estimate possible impacts from hemlock loss in GSMNP, we paired hardwood- and hemlock-dominated streams to examine differences in water temperature, nitrate concentrations, pH, discharge, and available photosynthetic light. We used a Geographic Information System (GIS) to identify stream pairs that were similar in topography, geology, land use, and disturbance history in order to isolate forest type as a variable. Differences between hemlock- and hardwood-dominated streams could not be explained by dominant forest type alone as forest type yields no consistent signal on measured conditions of headwater streams in GSMNP. The variability in the results indicate that other landscape variables, such as the influence of understory Rhododendron species, may exert more control on stream conditions than canopy composition. The results of this study suggest that the replacement of hemlock overstory with hardwood species will have minimal impact on long-term stream conditions, however disturbance during the transition is likely to have significant impacts. Management of riparian forests undergoing hemlock decline should, therefore, focus on facilitating a faster transition to hardwood-dominated stands to minimize long-term effects on water quality

Two-photon parametric pumping versus two-photon absorption: A quantum jump approach

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