A Fast and Compact Quantum Random Number Generator

We present the realization of a physical quantum random number generator based on the process of splitting a beam of photons on a beam splitter, a quantum mechanical source of true randomness. By utilizing either a beam splitter or a polarizing beam splitter, single photon detectors and high speed electronics the presented devices are capable of generating a binary random signal with an autocorrelation time of 11.8 ns and a continuous stream of random numbers at a rate of 1 Mbit/s. The randomness of the generated signals and numbers is shown by running a series of tests upon data samples. The devices described in this paper are built into compact housings and are simple to operate.Comment: 23 pages, 6 Figs. To appear in Rev. Sci. Inst

Functional Data Analysis of Amplitude and Phase Variation

The abundance of functional observations in scientific endeavors has led to a significant development in tools for functional data analysis (FDA). This kind of data comes with several challenges: infinite-dimensionality of function spaces, observation noise, and so on. However, there is another interesting phenomena that creates problems in FDA. The functional data often comes with lateral displacements/deformations in curves, a phenomenon which is different from the height or amplitude variability and is termed phase variation. The presence of phase variability artificially often inflates data variance, blurs underlying data structures, and distorts principal components. While the separation and/or removal of phase from amplitude data is desirable, this is a difficult problem. In particular, a commonly used alignment procedure, based on minimizing the $\mathbb{L}^2$ norm between functions, does not provide satisfactory results. In this paper we motivate the importance of dealing with the phase variability and summarize several current ideas for separating phase and amplitude components. These approaches differ in the following: (1) the definition and mathematical representation of phase variability, (2) the objective functions that are used in functional data alignment, and (3) the algorithmic tools for solving estimation/optimization problems. We use simple examples to illustrate various approaches and to provide useful contrast between them.Comment: Published at http://dx.doi.org/10.1214/15-STS524 in the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Joint and individual analysis of breast cancer histologic images and genomic covariates

A key challenge in modern data analysis is understanding connections between complex and differing modalities of data. For example, two of the main approaches to the study of breast cancer are histopathology (analyzing visual characteristics of tumors) and genetics. While histopathology is the gold standard for diagnostics and there have been many recent breakthroughs in genetics, there is little overlap between these two fields. We aim to bridge this gap by developing methods based on Angle-based Joint and Individual Variation Explained (AJIVE) to directly explore similarities and differences between these two modalities. Our approach exploits Convolutional Neural Networks (CNNs) as a powerful, automatic method for image feature extraction to address some of the challenges presented by statistical analysis of histopathology image data. CNNs raise issues of interpretability that we address by developing novel methods to explore visual modes of variation captured by statistical algorithms (e.g. PCA or AJIVE) applied to CNN features. Our results provide many interpretable connections and contrasts between histopathology and genetics

On Hirschman and log-Sobolev inequalities in mu-deformed Segal-Bargmann analysis

We consider a deformation of Segal-Bargmann space and its transform. We study L^p properties of this transform and obtain entropy-entropy inequalities (Hirschman) and entropy-energy inequalities (log-Sobolev) that generalize the corresponding known results in the undeformed theory.Comment: 42 pages, 3 figure

BlackOPs: Increasing confidence in variant detection through mappability filtering

Identifying variants using high-throughput sequen-cing data is currently a challenge because true biological variants can be indistinguishable from technical artifacts. One source of technical arti-fact results from incorrectly aligning experimen-tally observed sequences to their true genomic origin (‘mismapping’) and inferring differences in mismapped sequences to be true variants. We de-veloped BlackOPs, an open-source tool that simu-lates experimental RNA-seq and DNA whole exome sequences derived from the reference genome, aligns these sequences by custom parameters, detects variants and outputs a blacklist of positions and alleles caused by mismapping. Blacklist

Outcomes of off-label drug uses in hospitals: a multicentric prospective study

Purpose: The study aims to assess the clinical evidence, outcome and cost of off-label use of medicines in the hospital setting. Methods: A multicentric prospective cohort study of patients treated with off-label medicines was carried out in five tertiary hospitals from May 2011 to May 2012. Information on clinical characteristics of patients, drugs, outcomes and costs was collected. Patients were followed up to 6 months, and information was assessed by reviewing clinical records and interviewing physicians. Results: A total of 226 patients were included. The median (interquartile range (IQR)) age of patients was 46 (3362) years; 59 % were women. Patients had received a median of three previous treatments, and a lack of response (or suboptimal) was the main reason for off-label use (72.1 %). A total of 232 off-label medicines were administered for 102 different indications. The most frequent medicines were rituximab (49; 21.1 %), botulinum toxin (25; 10.7 %) and omalizumab (14; 6.0 %). In 117 (51.8 %) cases, the level of clinical evidence for their use was low. A partial clinical response was observed in 82 patients (36.3 %), complete response in 71 (31.4 %) and stabilization in 11 (4.9 %). A total of 58 (26.5 %) patients had adverse effects, which in 11 (4.9 %) were severe. The median (IQR) cost per patient was 2,943.07 (541.95,872.54). Conclusions: There was a high variability of off-label medicines and indications. Although the clinical evidence of off-label medicines was often low, clinical response was observed in many patients with previous multiple treatment failure, but at the expense of some adverse effects and a high cost. Registers of patients would be helpful for clinical decisions, although clinical trials are needed

On the kinetic systems for simple reacting spheres : modeling and linearized equations

Series: Springer Proceedings in Mathematics & Statistics, Vol. 75In this work we present some results on the kinetic theory of chemically reacting gases, concerning the model of simple reacting spheres (SRS) for a gaseous mixture undergoing a chemical reaction of type A1 +A2 A3 +A4. Starting from the approach developed in paper [11], we provide properties of the SRS system needed in the mathematical and physical analysis of the model. Our main result in this proceedings provides basic properties of the SRS system linearized around the equilibrium, including the explicit representations of the kernels of the linearized SRS operators.Fundação para a Ciência e a Tecnologia (FCT), PEst-C/MAT/UI0013/2011, SFRH/BD/28795/200

SigFuge: Single gene clustering of RNA-seq reveals differential isoform usage among cancer samples

High-throughput sequencing technologies, including RNA-seq, have made it possible to move beyond gene expression analysis to study transcriptional events including alternative splicing and gene fusions. Furthermore, recent studies in cancer have suggested the importance of identifying transcriptionally altered loci as biomarkers for improved prognosis and therapy. While many statistical methods have been proposed for identifying novel transcriptional events with RNA-seq, nearly all rely on contrasting known classes of samples, such as tumor and normal. Few tools exist for the unsupervised discovery of such events without class labels. In this paper, we present SigFuge for identifying genomic loci exhibiting differential transcription patterns across many RNA-seq samples. SigFuge combines clustering with hypothesis testing to identify genes exhibiting alternative splicing, or differences in isoform expression. We apply SigFuge to RNA-seq cohorts of 177 lung and 279 head and neck squamous cell carcinoma samples from the Cancer Genome Atlas, and identify several cases of differential isoform usage including CDKN2A, a tumor suppressor gene known to be inactivated in a majority of lung squamous cell tumors. By not restricting attention to known sample stratifications, SigFuge offers a novel approach to unsupervised screening of genetic loci across RNA-seq cohorts. SigFuge is available as an R package through Bioconductor

Smoke gets in your eyes:what is sociological about cigarettes?

Contemporary public health approaches increasingly draw attention to the unequal social distribution of cigarette smoking. In contrast, critical accounts emphasize the importance of smokers’ situated agency, the relevance of embodiment and how public health measures against smoking potentially play upon and exacerbate social divisions and inequality. Nevertheless, if the social context of cigarettes is worthy of such attention, and sociology lays a distinct claim to understanding the social, we need to articulate a distinct, positive and systematic claim for smoking as an object of sociological enquiry. This article attempts to address this by situating smoking across three main dimensions of sociological thinking: history and social change; individual agency and experience; and social structures and power. It locates the emergence and development of cigarettes in everyday life within the project of modernity of the nineteenth and twentieth centuries. It goes on to assess the habituated, temporal and experiential aspects of individual smoking practices in everyday lifeworlds. Finally, it argues that smoking, while distributed in important ways by social class, also works relationally to render and inscribe it