Analyzing in situ gene expression in the mouse brain with image registration, feature extraction and block clustering

Background: Many important high throughput projects use in situ hybridization and may require the analysis of images of spatial cross sections of organisms taken with cellular level resolution. Projects creating gene expression atlases at unprecedented scales for the embryonic fruit fly as well as the embryonic and adult mouse already involve the analysis of hundreds of thousands of high resolution experimental images mapping mRNA expression patterns. Challenges include accurate registration of highly deformed tissues, associating cells with known anatomical regions, and identifying groups of genes whose expression is coordinately regulated with respect to both concentration and spatial location. Solutions to these and other challenges will lead to a richer understanding of the complex system aspects of gene regulation in heterogeneous tissue. Results: We present an end-to-end approach for processing raw in situ expression imagery and performing subsequent analysis. We use a non-linear, information theoretic based image registration technique specifically adapted for mapping expression images to anatomical annotations and a method for extracting expression information within an anatomical region. Our method consists of coarse registration, fine registration, and expression feature extraction steps. From this we obtain a matrix for expression characteristics with rows corresponding to genes and columns corresponding to anatomical sub-structures. We perform matrix block cluster analysis using a novel row-column mixture model and we relate clustered patterns to Gene Ontology (GO) annotations. Conclusion: Resulting registrations suggest that our method is robust over intensity levels and shape variations in ISH imagery. Functional enrichment studies from both simple analysis and block clustering indicate that gene relationships consistent with biological knowledge of neuronal gene functions can be extracted from large ISH image databases such as the Allen Brain Atlas [1] and the Max-Planck Institute [2] using our method. While we focus here on imagery and experiments of the mouse brain our approach should be applicable to a variety of in situ experiments

Pennsylvania Folklife Vol. 11, No. 1

• A Dunker Weekend Love Feast of 100 Years Ago • The Peacock in Pennsylvania • The Get-Togethers of the Young Amish Folk • Church and Meetinghouse Stables and Sheds • Abraham Harley Cassel - Dunkard Bibliophile • Mennonite Folklore • Springs and Springhouses • Finishing Wooden Surfaces • Early Funeral Notices • Collecting Dialect Folk Songshttps://digitalcommons.ursinus.edu/pafolklifemag/1006/thumbnail.jp

A Year of Wavefront Sensing with JWST in Flight: Cycle 1 Telescope Monitoring and Maintenance Summary

We summarize JWST's measured telescope performance across science Cycle 1. The stability of segments alignments is typically better than 10 nanometers RMS between measurements every two days, leading to highly stable point spread functions. The frequency of segment "tilt events" decreased significantly, and larger tilt events ceased entirely, as structures gradually equilibrated after cooldown. Mirror corrections every 1-2 months now maintain the telescope below 70 nm RMS wavefront error. Observed micrometeoroid impacts during cycle 1 had negligible effect on science performance, consistent with preflight predictions. As JWST begins Cycle 2, its optical performance and stability are equal to, and in some ways better than, the performance reported at the end of commissioning.Comment: STScI Technical Memo. 2.5 pages text, 1 figur

Applied Plasma Research

Contains research objectives, summary of research and reports on four research projects.National Science Foundation (Grant GK-28282X1)National Science Foundation (Grant GK-33843

Plasma Dynamics

Contains research objectives and summary of research on twenty-one projects split into three sections, with four sub-sections in the second section and reports on twelve research projects.National Science Foundation (Grant ENG75-06242)U.S. Energy Research and Development Administration (Contract E(11-1)-2766)U.S. Energy Research and Development Agency (Contract E(11-1)-3070)U.S. Energy Research and Development Administration (Contract E(11-1)-3070)Research Laboratory of Electronics, M.I.T. Industrial Fellowshi

Plasma Dynamics

Contains reports on seventeen research projects split into two sections.National Science Foundation (Grant ENG77-00340)U. S. Energy Research and Development Administration (Contract E(11-1)-2766)U. S. Energy Research and Development Administration (Contract EY-76-S-02-2766)U. S. Air Force - Office of Scientific Research (Grant AFOSR-77-3143)U. S. Department of Energy (Grant EG-77-G-01-4107

Plasma Dynamics

Contains research objectives and summary of research on nineteen research projects split into five sections.National Science Foundation (Grant ENG75-06242-A01)U.S. Energy Research and Development Administration (Contract E(11-1)-2766)U.S. Air Force - Office of Scientific Research (Grant AFOSR-77-3143)U.S. Energy Research and Development Administration (Contract EY-76-C2-02-3070.*000

Plasma Dynamics

Contains research objectives and summary of research on eighteen research projects split into seven sections and reports on four research projects.U.S. Atomic Energy Commission (Contract AT(l1-1)-3070)National Science Foundation (Grant GK-37979X1

The James Webb Space Telescope Mission: Optical Telescope Element Design, Development, and Performance

The James Webb Space Telescope (JWST) is a large, infrared space telescope that has recently started its science program which will enable breakthroughs in astrophysics and planetary science. Notably, JWST will provide the very first observations of the earliest luminous objects in the Universe and start a new era of exoplanet atmospheric characterization. This transformative science is enabled by a 6.6 m telescope that is passively cooled with a 5-layer sunshield. The primary mirror is comprised of 18 controllable, low areal density hexagonal segments, that were aligned and phased relative to each other in orbit using innovative image-based wavefront sensing and control algorithms. This revolutionary telescope took more than two decades to develop with a widely distributed team across engineering disciplines. We present an overview of the telescope requirements, architecture, development, superb on-orbit performance, and lessons learned. JWST successfully demonstrates a segmented aperture space telescope and establishes a path to building even larger space telescopes.Comment: accepted by PASP for JWST Overview Special Issue; 34 pages, 25 figure

Protein disulphide isomerase-assisted functionalization of proteinaceous substrates

Protein disulphide isomerase (PDI) is an enzyme that catalyzes thiol-disulphide exchange reactions among a broad spectrum of substrates, including proteins and low-molecular thiols and disulphides. As the first protein-folding catalyst reported, the study of PDI has mainly involved the correct folding of several cysteine-containing proteins. Its application on the functionalization of protein-based materials has not been extensively reported. Herein, we review the applications of PDI on the modification of proteinaceous substrates and discuss its future potential. The mechanism involved in PDI functionalization of fibrous protein substrates is discussed in detail. These approaches allow innovative applications in textile dyeing and finishing, medical textiles, controlled drug delivery systems and hair or skin care products.We thank to FCT 'Fundacao para a Ciencia e Tecnologia' (scholarship SFRH/BD/38363/2007) for providing Margarida Fernandes the grant for PhD studies