A method for comparing non-nested models with application to astrophysical searches for new physics

Searches for unknown physics and decisions between competing astrophysical models to explain data both rely on statistical hypothesis testing. The usual approach in searches for new physical phenomena is based on the statistical Likelihood Ratio Test (LRT) and its asymptotic properties. In the common situation, when neither of the two models under comparison is a special case of the other i.e., when the hypotheses are non-nested, this test is not applicable. In astrophysics, this problem occurs when two models that reside in different parameter spaces are to be compared. An important example is the recently reported excess emission in astrophysical $\gamma$-rays and the question whether its origin is known astrophysics or dark matter. We develop and study a new, simple, generally applicable, frequentist method and validate its statistical properties using a suite of simulations studies. We exemplify it on realistic simulated data of the Fermi-LAT $\gamma$-ray satellite, where non-nested hypotheses testing appears in the search for particle dark matter.Comment: We welcome examples of non-nested models testing problem

Perceived occlusion and comfort in receiver-in-the-ear hearing aids

Purpose: In this study participants rated self-perceived occlusion and physical comfort for receiver-in-the-ear (RITE) hearing aids with different sizes of standard domes. Perceived occlusion was rated across listening and own voice conditions. Method: Twenty-one older adults with hearing impairment were fitted with bilateral RITE hearing aids and tested with three dome size conditions: open, plus, and power domes, and one control condition: the participants\u27 own aids. Participants ranked self-perceived occlusion across the dome size conditions as well as across listening and own voice conditions, and also ranked level of physical comfort across dome sizes. Results: Self-perceived occlusion increased as dome size increased, with the open domes and participants\u27 own aids causing the least amount of occlusion. The own voice condition yielded the most significant results, although significance was found across the listening condition as well. Perceived physical comfort decreased as dome size increased. Conclusions: Self-perceived occlusion was greatest for the power domes, although average level of occlusion did not exceed moderate occlusion. Perceived physical comfort was highest with the open dome and participants\u27 own aids. Plus and power domes were respectively ranked as more uncomfortable than the open domes, but overall were more comfortable than uncomfortable

On methods for correcting for the look-elsewhere effect in searches for new physics

The search for new significant peaks over a energy spectrum often involves a statistical multiple hypothesis testing problem. Separate tests of hypothesis are conducted at different locations producing an ensemble of local p-values, the smallest of which is reported as evidence for the new resonance. Unfortunately, controlling the false detection rate (type I error rate) of such procedures may lead to excessively stringent acceptance criteria. In the recent physics literature, two promising statistical tools have been proposed to overcome these limitations. In 2005, a method to "find needles in haystacks" was introduced by Pilla et al. [1], and a second method was later proposed by Gross and Vitells [2] in the context of the "look elsewhere effect" and trial factors. We show that, for relatively small sample sizes, the former leads to an artificial inflation of statistical power that stems from an increase in the false detection rate, whereas the two methods exhibit similar performance for large sample sizes. We apply the methods to realistic simulations of the Fermi Large Area Telescope data, in particular the search for dark matter annihilation lines. Further, we discuss the counter-intutive scenario where the look-elsewhere corrections are more conservative than much more computationally efficient corrections for multiple hypothesis testing. Finally, we provide general guidelines for navigating the tradeoffs between statistical and computational efficiency when selecting a statistical procedure for signal detection

Desmin forms toxic, seeding-competent amyloid aggregates that persist in muscle fibers

Desmin-associated myofibrillar myopathy (MFM) has pathologic similarities to neurodegeneration-associated protein aggregate diseases. Desmin is an abundant muscle-specific intermediate filament, and disease mutations lead to its aggregation in cells, animals, and patients. We reasoned that similar to neurodegeneration-associated proteins, desmin itself may form amyloid. Desmin peptides corresponding to putative amyloidogenic regions formed seeding-competent amyloid fibrils. Amyloid formation was increased when disease-associated mutations were made within the peptide, and this conversion was inhibited by the anti-amyloid compound epigallocatechin-gallate. Moreover, a purified desmin fragment (aa 117 to 348) containing both amyloidogenic regions formed amyloid fibrils under physiologic conditions. Desmin fragment-derived amyloid coaggregated with full-length desmin and was able to template its conversion into fibrils in vitro. Desmin amyloids were cytotoxic to myotubes and disrupted their myofibril organization compared with desmin monomer or other nondesmin amyloids. Finally, desmin fragment amyloid persisted when introduced into mouse skeletal muscle. These data suggest that desmin forms seeding-competent amyloid that is toxic to myofibers. Moreover, small molecules known to interfere with amyloid formation and propagation may have therapeutic potential in MFM

Sequential hypothesis testing for Axion Haloscopes

The goal of this paper is to introduce a novel likelihood-based inferential framework for axion haloscopes which is valid under the commonly applied "rescanning" protocol. The proposed method enjoys short data acquisition times and a simple tuning of the detector configuration. Local statistical significance and power are computed analytically, avoiding the need of burdensome simulations. Adequate corrections for the look-elsewhere effect are also discussed. The performance of our inferential strategy is compared with that of a simple method which exploits the geometric probability of rescan. Finally, we exemplify the method with an application to a HAYSTAC type axion haloscope.Comment: 14 pages, 12 figure

Functional Gene Networks: R/Bioc package to generate and analyse gene networks derived from functional enrichment and clustering

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License.Functional Gene Networks (FGNet) is an R/Bioconductor package that generates gene networks derived from the results of functional enrichment analysis (FEA) and annotation clustering. The sets of genes enriched with specific biological terms (obtained from a FEA platform) are transformed into a network by establishing links between genes based on common functional annotations and common clusters. The network provides a new view of FEA results revealing gene modules with similar functions and genes that are related to multiple functions. In addition to building the functional network, FGNet analyses the similarity between the groups of genes and provides a distance heatmap and a bipartite network of functionally overlapping genes. The application includes an interface to directly perform FEA queries using different external tools: DAVID, GeneTerm Linker, TopGO or GAGE; and a graphical interface to facilitate the use.This work was supported by the “Accion Estrategica en Salud” (AES) of the “Instituto de Salud Carlos III” (ISCiii) from the Spanish Government (projects granted to J.D.L.R.: PS09/00843 and PI12/00624); and by the “Consejeria de Educación” of the “Junta Castilla y León” (JCyL) and the European Social Fund (ESF) with grants given to S.A. and C.D.Peer Reviewe