EMAGE: a spatial database of gene expression patterns during mouse embryo development

EMAGE () is a freely available, curated database of gene expression patterns generated by in situ techniques in the developing mouse embryo. It is unique in that it contains standardized spatial representations of the sites of gene expression for each gene, denoted against a set of virtual reference embryo models. As such, the data can be interrogated in a novel and abstract manner by using space to define a query. Accompanying the spatial representations of gene expression patterns are text descriptions of the sites of expression, which also allows searching of the data by more conventional text-based methods

EMAGE: a spatial database of gene expression patterns during mouse embryo development

EMAGE () is a freely available, curated database of gene expression patterns generated by in situ techniques in the developing mouse embryo. It is unique in that it contains standardized spatial representations of the sites of gene expression for each gene, denoted against a set of virtual reference embryo models. As such, the data can be interrogated in a novel and abstract manner by using space to define a query. Accompanying the spatial representations of gene expression patterns are text descriptions of the sites of expression, which also allows searching of the data by more conventional text-based methods

Constraining the Absolute Orientation of Eta Carinae's Binary Orbit: A 3-D Dynamical Model for the Broad [Fe III] Emission

We present a three-dimensional (3-D) dynamical model for the broad [Fe III] emission observed in Eta Carinae using the Hubble Space Telescope/Space Telescope Imaging Spectrograph (HST/STIS). This model is based on full 3-D Smoothed Particle Hydrodynamics (SPH) simulations of Eta Car's binary colliding winds. Radiative transfer codes are used to generate synthetic spectro-images of [Fe III] emission line structures at various observed orbital phases and STIS slit position angles (PAs). Through a parameter study that varies the orbital inclination i, the PA {\theta} that the orbital plane projection of the line-of-sight makes with the apastron side of the semi-major axis, and the PA on the sky of the orbital axis, we are able, for the first time, to tightly constrain the absolute 3-D orientation of the binary orbit. To simultaneously reproduce the blue-shifted emission arcs observed at orbital phase 0.976, STIS slit PA = +38 degrees, and the temporal variations in emission seen at negative slit PAs, the binary needs to have an i \approx 130 to 145 degrees, {\theta} \approx -15 to +30 degrees, and an orbital axis projected on the sky at a PA \approx 302 to 327 degrees east of north. This represents a system with an orbital axis that is closely aligned with the inferred polar axis of the Homunculus nebula, in 3-D. The companion star, Eta B, thus orbits clockwise on the sky and is on the observer's side of the system at apastron. This orientation has important implications for theories for the formation of the Homunculus and helps lay the groundwork for orbital modeling to determine the stellar masses.Comment: 23 pages, 12 color figures, plus 2 online-only appendices (available in the /anc folder of the Source directory). Accepted for publication in MNRA

A spectroscopic event of eta Car viewed from different directions: The data and first results

We present spectroscopic observations with high spectral resolution of eta Car as seen by the SE lobe of the Homunculus nebula over the 2003.5 "spectroscopic event". The observed spectra represent the stellar spectrum emitted near the pole of the star and are much less contaminated with nebular emission lines than direct observations of the central object. The "event" is qualitatively similar near the pole to what is observed in direct spectra of the star (more equator-on at 45 degree), but shows interesting differences. The observations show that the equivalent width changes of H alpha emission and other lines are less pronounced at the pole than in the line of sight. Also the absorption components appear less variable. A pronounced high-velocity absorption is present near the event in the He I lines indicating a mass-ejection event. This feature is also seen, but less pronounced, in the hydrogen lines. HeII4686 emission is observed for a brief period of time near the event and appears, if corrected for light travel time, to precede similar emission in the direct view. Our observations indicate that the event is probably not only a change in ionization and excitation structure or a simple eclipse-like event.Comment: 10 pages, 16 figures, accepted by A&

A Methodology for Risk Assessment to Improve the Resilience and Sustainability of Critical Infrastructure with Case Studies from the United States Army

Reliable performance of energy and water infrastructure is central to the mission readiness of the United States Army. These systems are vulnerable to coordinated attacks from an adversary as well as disruption from natural events. The objectives of this work were to investigate Army installations in North America, identify best practices for improving the resilience and sustainability of critical energy and water infrastructure, and develop a framework and methodology for analyzing the resilience of an installation under varying outage scenarios. This work was accomplished using a multi-layered decision process to identify unique case studies from the 117 active-duty domestic Army installations. A framework for analyzing and assessing the resilience of an installation was then developed to help inform stakeholders. Metered energy and water data from buildings across Fort Benning, GA were curated to inform the modeling framework, including a discrete-event simulation of the supply and demand for energy and water on the installation using ProModel. This simulation was used to study the scale of solutions required to address outage events of varying frequency, duration, and magnitude, the combination of which is described as the severity of outages at a given site. This project helps develop a framework to inform how installations might meet Army Directive 2020-03, which states that installations must be able to sustain mission requirements for a minimum of 14 days after a disruption has occurred

Revisiting 2D Numerical Models for the 19th century outbursts of η\eta Carinae

We present here new results of two-dimensional hydrodynamical simulations of the eruptive events of the 1840s (the great) and the 1890s (the minor) eruptions suffered by the massive star $\eta$ Car. The two bipolar nebulae commonly known as the Homunculus and the little Homunculus were formed from the interaction of these eruptive events with the underlying stellar wind. As in previous work (Gonzalez et al. 2004a, 2004b), we assume here an interacting, nonspherical multiple-phase wind scenario to explain the shape and the kinematics of both Homunculi, but adopt a more realistic parametrization of the phases of the wind. During the 1890s eruptive event, the outflow speed {\it decreased} for a short period of time. This fact suggests that the little Homunculus is formed when the eruption ends, from the impact of the post-outburst $\eta$ Car wind (that follows the 1890s event) with the eruptive flow (rather than by the collision of the eruptive flow with the pre-outburst wind, as claimed in previous models; Gonzalez et al. 2004a, 2004b). Our simulations reproduce quite well the shape and the observed expansion speed of the large Homunculus. The little Homunculus (which is embedded within the large Homunculus) becomes Rayleigh-Taylor unstable and develop filamentary structures that resembles the spatial features observed in the polar caps. In addition, we find that the interior cavity between the two Homunculi is partially filled by material that is expelled during the decades following the great eruption. This result may be connected with the observed double-shell structure in the polar lobes of the $\eta$ Car nebula. Finally, as in previous work, we find the formation of tenuous, equatorial, high-speed features that seem to be related to the observed equatorial skirt of $\eta$ Car.Comment: accepted for publication in MNRA

Organization of the pronephric kidney revealed by large-scale gene expression mapping

Gene expression mapping reveals 8 functionally distinct domains in the Xenopus pronephros. Interestingly, no structure equivalent to the mammalian collecting duct is identified

EMAGE—Edinburgh Mouse Atlas of Gene Expression: 2008 update

EMAGE (http://genex.hgu.mrc.ac.uk/Emage/database) is a database of in situ gene expression patterns in the developing mouse embryo. Domains of expression from raw data images are spatially integrated into a set of standard 3D virtual mouse embryos at different stages of development, allowing data interrogation by spatial methods. Sites of expression are also described using an anatomy ontology and data can be queried using text-based methods. Here we describe recent enhancements to EMAGE which include advances in spatial search methods including: a refined local spatial similarity search algorithm, a method to allow global spatial comparison of patterns in EMAGE and subsequent hierarchical-clustering, and spatial searches across multiple stages of development. In addition, we have extended data access by the introduction of web services and new HTML-based search interfaces, which allow access to data that has not yet been spatially annotated. We have also started incorporating full 3D images of gene expression that have been generated using optical projection tomography (OPT)