Transforming a 4th year Modern Optics Course Using a Deliberate Practice Framework

We present a study of active learning pedagogies in an upper division physics course. This work was guided by the principle of deliberate practice for the development of expertise, and this principle was used in the design of the materials and the orchestration of the classroom activities of the students. We present our process for efficiently converting a traditional lecture course based on instructor notes into activities for such a course with active learning methods. Ninety percent of the same material was covered and scores on common exam problems showed a 15 % improvement with an effect size greater than 1 after the transformation. We observe that the improvement and the associated effect size is sustained after handing off the materials to a second instructor. Because the improvement on exam questions was independent of specific problem topics and because the material tested was so mathematically advanced and broad (including linear algebra, Fourier Transforms, partial differential equations, vector calculus), we expect the transformation process could be applied to most upper division physics courses having a similar mathematical base.Comment: 31 page

Emergent Orientation Selectivity from Random Networks in Mouse Visual Cortex

The connectivity principles underlying the emergence of orientation selectivity in primary visual cortex (V1) of mammals lacking an orientation map (such as rodents and lagomorphs) are poorly understood. We present a computational model in which random connectivity gives rise to orientation selectivity that matches experimental observations. The model predicts that mouse V1 neurons should exhibit intricate receptive fields in the two-dimensional frequency domain, causing a shift in orientation preferences with spatial frequency. We find evidence for these features in mouse V1 using calcium imaging and intracellular whole-cell recordings. Pattadkal et al. show that orientation selectivity can emerge from random connectivity, and offer a distinct perspective for how computations occur in the neocortex. They propose that a random convergence of inputs can provide signals for orientation preference in contrast with the dominant model that requires a precise arrangement.Fil: Pattadkal, Jagruti J.. University of Texas at Austin; Estados UnidosFil: Mato, German. Comisión Nacional de Energía Atómica. Gerencia del Área de Energía Nuclear. Instituto Balseiro; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: van Vreeswijk, Carl. Centre National de la Recherche Scientifique; FranciaFil: Priebe, Nicholas J.. University of Texas at Austin; Estados UnidosFil: Hansel, David. Centre National de la Recherche Scientifique; Franci

Modeling and visualizing uncertainty in gene expression clusters using Dirichlet process mixtures

Although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data, little attention has been paid to uncertainty in the results obtained. Dirichlet process mixture (DPM) models provide a nonparametric Bayesian alternative to the bootstrap approach to modeling uncertainty in gene expression clustering. Most previously published applications of Bayesian model-based clustering methods have been to short time series data. In this paper, we present a case study of the application of nonparametric Bayesian clustering methods to the clustering of high-dimensional nontime series gene expression data using full Gaussian covariances. We use the probability that two genes belong to the same cluster in a DPM model as a measure of the similarity of these gene expression profiles. Conversely, this probability can be used to define a dissimilarity measure, which, for the purposes of visualization, can be input to one of the standard linkage algorithms used for hierarchical clustering. Biologically plausible results are obtained from the Rosetta compendium of expression profiles which extend previously published cluster analyses of this data

Synthesis, structures and cytotoxicity studies of p-sulfonatocalix[4]arene lanthanide complexes

A number of p-sulfonatocalix[4]arene complexes of the lanthanides (Tb, Gd, and Eu) have been prepared, some in the presence of tetraazamacrocycle 1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid (DO3A), and fully characterised. Crystal structure determinations reveal lanthanide coordination at the sulfonate group, bridging several calixarene units, giving coordination polymers. All complexes in this study have been determined to be relatively non-toxic using in vitro cell assays with CC₅₀ values in the range 30–170 μM

Engineering recombinant orsay virus directly in the metazoan host Caenorhabditis elegans

The recent identification of Orsay virus, the first virus that is capable of naturally infecting Caenorhabditis elegans, provides a unique opportunity to explore host-virus interaction studies in this invaluable model organism. A key feature of this system is the robust genetic tractability of the host, C. elegans, which would ideally be complemented by the ability to genetically manipulate Orsay virus in parallel. To this end, we developed a plasmid-based reverse genetics system for Orsay virus by creating transgenic C. elegans strains harboring Orsay virus cDNAs. Both wild-type and mutant Orsay viruses, including a FLAG epitope-tagged recombinant Orsay virus, were generated by use of the reverse genetics system. This is the first plasmid-based virus reverse genetics system in the metazoan C. elegans. The Orsay virus reverse genetics we established will serve as a fundamental tool in host-virus interaction studies in the model organism C. elegans. IMPORTANCE To date, Orsay virus is the first and the only identified virus capable of naturally infecting Caenorhabditis elegans. C. elegans is a simple multicellular model organism that mimics many fundamental features of human biology and has been used to define many biological properties conserved through evolution. Thus, the Orsay virus-C. elegans infection system provides a unique opportunity to study host-virus interactions. In order to take maximal advantage of this system, the ability to genetically engineer mutant forms of Orsay virus would be highly desirable. Most efforts to engineer viruses have been done with cultured cells. Here we describe the creation of mutant viruses directly in the multicellular organism C. elegans without the use of cell culture. We engineered a virus expressing a genetically tagged protein that could be detected in C. elegans. This provides proof of concept for modifying Orsay virus, which will greatly facilitate studies in this experimental system