An Oral History of Marie O. Ronen, a One-Room Schoolteacher

A transcript of an oral history of Marie O. Ronen, a one-room schoolteacher for Research in Education 803/https://scholars.fhsu.edu/ors/1290/thumbnail.jp

Implications of the Babinet Principle for Casimir Interactions

We formulate the Babinet Principle (BP) as a relation between the scattering amplitudes for electromagnetic waves, and combine it with multiple scattering techniques to derive new properties of Casimir forces. We show that the Casimir force exerted by a planar conductor or dielectric on a self- complementary perforated planar mirror is approximately half that on a uniform mirror independent of the distance between them. The BP suggests that Casimir edge effects are anomalously small, supporting results obtained earlier in special cases. Finally, we illustrate how the BP can be used to estimate Casimir forces between perforated planar mirrors

Artificial trapping of a stable high-density dipolar exciton fluid

We present compelling experimental evidence for a successful electrostatic trapping of two-dimensional dipolar excitons that results in stable formation of a well confined, high-density and spatially uniform dipolar exciton fluid. We show that, for at least half a microsecond, the exciton fluid sustains a density higher than the critical density for degeneracy if the exciton fluid temperature reaches the lattice temperature within that time. This method should allow for the study of strongly interacting bosons in two dimensions at low temperatures, and possibly lead towards the observation of quantum phase transitions of 2D interacting excitons, such as superfluidity and crystallization.Comment: 11 pages 4 figure

A-Model Correlators from the Coulomb Branch

We compute the contribution of discrete Coulomb vacua to A-Model correlators in toric Gauged Linear Sigma Models. For models corresponding to a compact variety, this determines the correlators at arbitrary genus. For non-compact examples, our results imply the surprising conclusion that the quantum cohomology relations break down for a subset of the correlators.Comment: 27 pages, 1 xy-pic figur

Retinal metric: a stimulus distance measure derived from population neural responses

The ability of the organism to distinguish between various stimuli is limited by the structure and noise in the population code of its sensory neurons. Here we infer a distance measure on the stimulus space directly from the recorded activity of 100 neurons in the salamander retina. In contrast to previously used measures of stimulus similarity, this "neural metric" tells us how distinguishable a pair of stimulus clips is to the retina, given the noise in the neural population response. We show that the retinal distance strongly deviates from Euclidean, or any static metric, yet has a simple structure: we identify the stimulus features that the neural population is jointly sensitive to, and show the SVM-like kernel function relating the stimulus and neural response spaces. We show that the non-Euclidean nature of the retinal distance has important consequences for neural decoding.Comment: 5 pages, 4 figures, to appear in Phys Rev Let

Toward a script theory of guidance in computer-supported collaborative learning

This article presents an outline of a script theory of guidance for computer-supported collaborative learning (CSCL). With its four types of components of internal and external scripts (play, scene, role, and scriptlet) and seven principles, this theory addresses the question how CSCL practices are shaped by dynamically re-configured internal collaboration scripts of the participating learners. Furthermore, it explains how internal collaboration scripts develop through participation in CSCL practices. It emphasizes the importance of active application of subject matter knowledge in CSCL practices, and it prioritizes transactive over non-transactive forms of knowledge application in order to facilitate learning. Further, the theory explains how external collaboration scripts modify CSCL practices and how they influence the development of internal collaboration scripts. The principles specify an optimal scaffolding level for external collaboration scripts and allow for the formulation of hypotheses about the fading of external collaboration scripts. Finally, the article points towards conceptual challenges and future research questions

LEDGF/p75 is critical but not essential for multiple-round HIV 1 replication

status: publishe

PiGx: reproducible genomics analysis pipelines with GNU Guix

In bioinformatics, as well as other computationally-intensive research fields, there is a need for workflows that can reliably produce consistent output, from known sources, independent of the software environment or configuration settings of the machine on which they are executed. Indeed, this is essential for controlled comparison between different observations or for the wider dissemination of workflows. Providing this type of reproducibility and traceability, however, is often complicated by the need to accommodate the myriad dependencies included in a larger body of software, each of which generally come in various versions. Moreover, in many fields (bioinformatics being a prime example), these versions are subject to continual change due to rapidly evolving technologies, further complicating problems related to reproducibility. Here, we propose a principled approach for building analysis pipelines and managing their dependencies with GNU Guix. As a case study to demonstrate the utility of our approach, we present a set of highly reproducible pipelines called PiGx for the analysis of RNA-seq, ChIP-seq, Bisulfite-seq, and single-cell RNA-seq. All pipelines process raw experimental data, and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables. Users may install these highly reproducible packages and apply them to their own datasets without any special computational expertise beyond the use of the command line. We hope such a toolkit will provide immediate benefit to laboratory workers wishing to process their own data sets or bioinformaticians seeking to automate all, or parts of, their analyses. In the long term, we hope our approach to reproducibility will serve as a blueprint for reproducible workflows in other areas. Our pipelines, along with their corresponding documentation and sample reports, are available at http://bioinformatics.mdc-berlin.de/pigx