Modeling dependent gene expression

In this paper we propose a Bayesian approach for inference about dependence of high throughput gene expression. Our goals are to use prior knowledge about pathways to anchor inference about dependence among genes; to account for this dependence while making inferences about differences in mean expression across phenotypes; and to explore differences in the dependence itself across phenotypes. Useful features of the proposed approach are a model-based parsimonious representation of expression as an ordinal outcome, a novel and flexible representation of prior information on the nature of dependencies, and the use of a coherent probability model over both the structure and strength of the dependencies of interest. We evaluate our approach through simulations and in the analysis of data on expression of genes in the Complement and Coagulation Cascade pathway in ovarian cancer.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS525 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Love is . . . an abstract word: the influence of phonological and semantic factors on verbal short-term memory in Williams syndrome

It has been claimed that verbal short-term memory in Williams syndrome is characterised by an over-use of phonological coding alongside a reduced contribution of lexical semantics. We critically examine this hypothesis and present results from a memory span task comparing performance on concrete and abstract words, together with a replication of a span task using phonologically similar and phonologically dissimilar words. Fourteen participants with Williams syndrome were individually matched to two groups of typically developing children. The first control group was matched on digit span and the second on vocabulary level. Significant effects were found for both the semantic and the phonological variables in the WS group as well as in the control groups, with no interaction between experimental variable and group in either experiment. The results demonstrate that, despite claims to the contrary, children and adults with WS are able to access and make use of lexical semantics in a verbal short-term memory task in a manner comparable to typically developing individuals

Phase-sensitive wavelength conversion based on cascaded quadratic processes in periodically poled lithium niobate waveguides

We propose and experimentally demonstrate a novel scheme of phase-sensitive wavelength conversion, based on a combination of cascaded second-order nonlinear effects in two cascaded periodically poled lithium niobate waveguides

Validation of a new instrument to guide and support insanity evaluations: the defendant’s insanity assessment support scale (DIASS)

The insanity defense represents one of the most controversial and debated evaluations performed by forensic psychiatrists and psychologists. Despite the variation among different jurisdictions, in Western countries, the legal standards for insanity often rely on the presence of cognitive and/or volitional impairment of the defendant at the time of the crime. We developed the defendant’s insanity assessment support scale (DIASS) based on a wide view of competent decision-making, which reflects core issues relevant to legal insanity in many jurisdictions. To assess the characteristics of the DIASS we asked 40 forensic experts (16% women; years of experience = 20.6 ± 12.9) to evaluate 10 real-life derived forensic cases with the DIASS; cases included defendants’ psychiatric symptom severity, evaluated through the 24-itemBrief Psychiatric Rating Scale (BPRS). Exploratory factor analysis by principal axis factoring was conducted, which disclosed a two-factor solution explaining 57.6% of the total variance. The DIASS showed a good internal consistency (Cronbach’s alpha = 0.86), and substantial inter-rater reliability (Cohen’s kappa = 0.72). The capacities analyzed through the DIASS were mainly affected by mania/excitement and psychotic dimensions in nonresponsible and with substantially diminished responsibility defendants, while by hostility and negative symptoms in responsible defendants. The DIASS proved to be an effective psychometric tool to guide and structure insanity defense evaluations, in order to improve their consistency and reliability

All-optical phase-regenerative multicasting of 40 Gbit/s DPSK signal in a degenerate phase sensitive amplifier

We demonstrate all-optical 1-to-5 differential phase-shift keyed (DPSK) wavelength multicasting at 40 Gbit/s using a degenerate four-wave mixing (FWM) based phase sensitive amplifier (PSA). Phase regenerative properties are reported with a sensitivity improvement of more that 10 dB

Saturation effects in degenerate phase sensitive fiber optic parametric amplifiers

We experimentally study saturation effects in degenerate phase sensitive amplifiers, revealing and explaining a gain regime suitable for all-optical signal processing functions such as phase regeneration

LIKELIHOOD ESTIMATION OF CONJUGACY RELATIONSHIPS IN LINEAR MODELS WITH APPLICATIONS TO HIGH-THROUGHPUT GENOMICS

In the simultaneous estimation of a large number of related quantities, multilevel models provide a formal mechanism for efficiently making use of the ensemble of information for deriving individual estimates. In this article we investigate the ability of the likelihood to identify the relationship between signal and noise in multilevel linear mixed models. Specifically, we consider the ability of the likelihood to diagnose conjugacy or independence between the signals and noises. Our work was motivated by the analysis of data from high-throughput experiments in genomics. The proposed model leads to a more flexible family. However, we further demonstrate that adequately capitalizing on the benefits of a well fitting fully-specified likelihood in the terms of gene ranking is difficult