Reply to Rouder (2014) : good frequentist properties raise confidence

Established psychological results have been called into question by demonstrations that statistical significance is easy to achieve, even in the absence of an effect. One often-warned-against practice, choosing when to stop the experiment on the basis of the results, is guaranteed to produce significant results. In response to these demonstrations, Bayes factors have been proposed as an antidote to this practice, because they are invariant with respect to how an experiment was stopped. Should researchers only care about the resulting Bayes factor, without concern for how it was produced? Yu, Sprenger, Thomas, and Dougherty (2014) and Sanborn and Hills (2014) demonstrated that Bayes factors are sometimes strongly influenced by the stopping rules used. However, Rouder (2014) has provided a compelling demonstration that despite this influence, the evidence supplied by Bayes factors remains correct. Here we address why the ability to influence Bayes factors should still matter to researchers, despite the correctness of the evidence. We argue that good frequentist properties mean that results will more often agree with researchers’ statistical intuitions, and good frequentist properties control the number of studies that will later be refuted. Both help raise confidence in psychological results

Bunburra Rockhole: Exploring the geology of a new differentiated basaltic asteroid

Bunburra Rockhole (BR) is the first recovered meteorite of the Desert Fireball Network. It was initially classified as a basaltic eucrite, based on texture, mineralogy, and mineral chemistry but subsequent O isotopic analyses showed that BR's composition lies significantly far away from the HED group of meteorites. This suggested that BR was not a piece of the HED parent body (4 Vesta), but other explanations could also account for the observed oxygen signatures. Possible scenarios include contamination by components from other bodies (chondrites or other achondrites) or that 4 Vesta may not be as equilibrated as hypothesized. After examining multiple pieces with different instruments (CT scans and x-ray maps), no obvious evidence of contamination was found. If BR is not from Vesta, a conundrum exists as no unusual features were found in mineral and bulk trace element chemistry as exist for other anomalous basaltic achondrites such as Ibitira or Asuka 881394. These meteorites have distinct petrological and geochemical characteristics, in addition to their anomalous O isotope compositions, that set them apart from eucrites. Thus, early results provided a somewhat ambiguous picture of BR's petrogenesis and parentage. To clarify the nature of the relationship, if any, between BR and eucrites, we have performed a correlated stable isotope and bulk chemical study of several lithologic fragments

Magnetic interactions of cold atoms with anisotropic conductors

We analyze atom-surface magnetic interactions on atom chips where the magnetic trapping potentials are produced by current carrying wires made of electrically anisotropic materials. We discuss a theory for time dependent fluctuations of the magnetic potential, arising from thermal noise originating from the surface. It is shown that using materials with a large electrical anisotropy results in a considerable reduction of heating and decoherence rates of ultra-cold atoms trapped near the surface, of up to several orders of magnitude. The trap loss rate due to spin flips is expected to be significantly reduced upon cooling the surface to low temperatures. In addition, the electrical anisotropy significantly suppresses the amplitude of static spatial potential corrugations due to current scattering within imperfect wires. Also the shape of the corrugation pattern depends on the electrical anisotropy: the preferred angle of the scattered current wave fronts can be varied over a wide range. Materials, fabrication, and experimental issues are discussed, and specific candidate materials are suggested.Comment: Selected as a Highlight paper in the European Physical Journal

Spin- and energy relaxation of hot electrons at GaAs surfaces

The mechanisms for spin relaxation in semiconductors are reviewed, and the mechanism prevalent in p-doped semiconductors, namely spin relaxation due to the electron-hole exchange interaction, is presented in some depth. It is shown that the solution of Boltzmann-type kinetic equations allows one to obtain quantitative results for spin relaxation in semiconductors that go beyond the original Bir-Aronov-Pikus relaxation-rate approximation. Experimental results using surface sensitive two-photon photoemission techniques show that the spin relaxation-time of electrons in p-doped GaAs at a semiconductor/metal surface is several times longer than the corresponding bulk spin relaxation-times. A theoretical explanation of these results in terms of the reduced density of holes in the band-bending region at the surface is presented.Comment: 33 pages, 12 figures; earlier submission replaced by corrected and expanded version; eps figures now included in the tex

The Minimum-Uncertainty Squeezed States for for Atoms and Photons in a Cavity

We describe a six-parameter family of the minimum-uncertainty squeezed states for the harmonic oscillator in nonrelativistic quantum mechanics. They are derived by the action of corresponding maximal kinematical invariance group on the standard ground state solution. We show that the product of the variances attains the required minimum value 1/4 only at the instances that one variance is a minimum and the other is a maximum, when the squeezing of one of the variances occurs. The generalized coherent states are explicitly constructed and their Wigner function is studied. The overlap coefficients between the squeezed, or generalized harmonic, and the Fock states are explicitly evaluated in terms of hypergeometric functions. The corresponding photons statistics are discussed and some applications to quantum optics, cavity quantum electrodynamics, and superfocusing in channeling scattering are mentioned. Explicit solutions of the Heisenberg equations for radiation field operators with squeezing are found.Comment: 27 pages, no figures, 174 references J. Phys. B: At. Mol. Opt. Phys., Special Issue celebrating the 20th anniversary of quantum state engineering (R. Blatt, A. Lvovsky, and G. Milburn, Guest Editors), May 201

Electron-electron scattering in linear transport in two-dimensional systems

We describe a method for numerically incorporating electron--electron scattering in quantum wells for small deviations of the distribution function from equilibrium, within the framework of the Boltzmann equation. For a given temperature $T$ and density $n$, a symmetric matrix needs to be evaluated only once, and henceforth it can be used to describe electron--electron scattering in any Boltzmann equation linear-response calculation for that particular $T$ and $n$. Using this method, we calculate the distribution function and mobility for electrons in a quantum-well, including full finite-temperature dynamic screening effects. We find that at some parameters which we investigated, electron--electron scattering reduces mobility by approximately 40\%.Comment: 12 pages, 2 figures (uuencoded

Integrating transposable elements in the 3D genome

Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, in this commentary we discuss its potential applicability to aspects of TE biology. Based on recent works on the relationship between genome organisation and TE integration, we argue that existing polymer models may be extended to create a predictive framework for the study of TE integration patterns. We suggest that these models may offer orthogonal and generic insights into the integration profiles (or "topography") of TEs across organisms. In addition, we provide simple polymer physics arguments and preliminary molecular dynamics simulations of TEs inserting into heterogeneously flexible polymers. By considering this simple model, we show how polymer folding and local flexibility may generically affect TE integration patterns. The preliminary discussion reported in this commentary is aimed to lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome

Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macro-evolution of a double-minute chromosome

In a glioblastoma tumour with multi-region sequencing before and after recurrence, we find an IDH1 mutation that is clonal in the primary but lost at recurrence. We also describe the evolution of a double-minute chromosome encoding regulators of the PI3K signalling axis that dominates at recurrence, emphasizing the challenges of an evolving and dynamic oncogenic landscape for precision medicin

myKaryoView: A Light-Weight Client for Visualization of Genomic Data

The Distributed Annotation System (DAS) is a protocol for easy sharing and integration of biological annotations. In order to visualize feature annotations in a genomic context a client is required. Here we present myKaryoView, a simple light-weight DAS tool for visualization of genomic annotation. myKaryoView has been specifically configured to help analyse data derived from personal genomics, although it can also be used as a generic genome browser visualization. Several well-known data sources are provided to facilitate comparison of known genes and normal variation regions. The navigation experience is enhanced by simultaneous rendering of different levels of detail across chromosomes. A simple interface is provided to allow searches for any SNP, gene or chromosomal region. User-defined DAS data sources may also be added when querying the system. We demonstrate myKaryoView capabilities for adding user-defined sources with a set of genetic profiles of family-related individuals downloaded directly from 23andMe. myKaryoView is a web tool for visualization of genomic data specifically designed for direct-to-consumer genomic data that uses publicly available data distributed throughout the Internet. It does not require data to be held locally and it is capable of rendering any feature as long as it conforms to DAS specifications. Configuration and addition of sources to myKaryoView can be done through the interface. Here we show a proof of principle of myKaryoView's ability to display personal genomics data with 23andMe genome data sources. The tool is available at: http://mykaryoview.com

CpG Islands Undermethylation in Human Genomic Regions under Selective Pressure

DNA methylation at CpG islands (CGIs) is one of the most intensively studied epigenetic mechanisms. It is fundamental for cellular differentiation and control of transcriptional potential. DNA methylation is involved also in several processes that are central to evolutionary biology, including phenotypic plasticity and evolvability. In this study, we explored the relationship between CpG islands methylation and signatures of selective pressure in Homo Sapiens, using a computational biology approach. By analyzing methylation data of 25 cell lines from the Encyclopedia of DNA Elements (ENCODE) Consortium, we compared the DNA methylation of CpG islands in genomic regions under selective pressure with the methylation of CpG islands in the remaining part of the genome. To define genomic regions under selective pressure, we used three different methods, each oriented to provide distinct information about selective events. Independently of the method and of the cell type used, we found evidences of undermethylation of CGIs in human genomic regions under selective pressure. Additionally, by analyzing SNP frequency in CpG islands, we demonstrated that CpG islands in regions under selective pressure show lower genetic variation. Our findings suggest that the CpG islands in regions under selective pressure seem to be somehow more “protected” from methylation when compared with other regions of the genome