GOES-R: Satellite Insight

GOES-R: Satellite Insight seeks to bring awareness of the GOES-R (Geostationary Operational Environmental Satellite -- R Series) satellite currently in development to an audience of all ages on the emerging medium of mobile games. The iPhone app (Satellite Insight) was created for the GOES-R Program. The app describes in simple terms the types of data products that can be produced from GOES-R measurements. The game is easy to learn, yet challenging for all audiences. It includes educational content and a path to further information about GOESR, its technology, and the benefits of the data it collects. The game features action-puzzle game play in which the player must prevent an overflow of data by matching falling blocks that represent different types of GOES-R data. The game adds more different types of data blocks over time, as long as the player can prevent a data overflow condition. Points are awarded for matches, and players can compete with themselves to beat their highest score

Space Place Prime

Space Place Prime is public engagement and education software for use on iPad. It targets a multi-generational audience with news, images, videos, and educational articles from the Space Place Web site and other NASA sources. New content is downloaded daily (or whenever the user accesses the app) via the wireless connection. In addition to the Space Place Web site, several NASA RSS feeds are tapped to provide new content. Content is retained for the previous several days, or some number of editions of each feed. All content is controlled on the server side, so features about the latest news, or changes to any content, can be made without updating the app in the Apple Store. It gathers many popular NASA features into one app. The interface is a boundless, slidable- in-any-direction grid of images, unique for each feature, and iconized as image, video, or article. A tap opens the feature. An alternate list mode presents menus of images, videos, and articles separately. Favorites can be tagged for permanent archive. Face - book, Twitter, and e-mail connections make any feature shareable

CometQuest: A Rosetta Adventure

This software is a higher-performance implementation of tiled WMS, with integral support for KML and time-varying data. This software is compliant with the Open Geospatial WMS standard, and supports KML natively as a WMS return type, including support for the time attribute. Regionated KML wrappers are generated that match the existing tiled WMS dataset. Ping and JPG formats are supported, and the software is implemented as an Apache 2.0 module that supports a threading execution model that is capable of supporting very high request rates. The module intercepts and responds to WMS requests that match certain patterns and returns the existing tiles. If a KML format that matches an existing pyramid and tile dataset is requested, regionated KML is generated and returned to the requesting application. In addition, KML requests that do not match the existing tile datasets generate a KML response that includes the corresponding JPG WMS request, effectively adding KML support to a backing WMS server

A comparative encyclopedia of DNA elements in the mouse genome

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases

IMC-Denoise: A content aware denoising pipeline to enhance Imaging Mass Cytometry

Imaging Mass Cytometry (IMC) is an emerging multiplexed imaging technology for analyzing complex microenvironments using more than 40 molecularly-specific channels. However, this modality has unique data processing requirements, particularly for patient tissue specimens where signal-to-noise ratios for markers can be low, despite optimization, and pixel intensity artifacts can deteriorate image quality and downstream analysis. Here we demonstrate an automated content-aware pipeline, IMC-Denoise, to restore IMC images deploying a differential intensity map-based restoration (DIMR) algorithm for removing hot pixels and a self-supervised deep learning algorithm for shot noise image filtering (DeepSNiF). IMC-Denoise outperforms existing methods for adaptive hot pixel and background noise removal, with significant image quality improvement in modeled data and datasets from multiple pathologies. This includes in technically challenging human bone marrow; we achieve noise level reduction of 87% for a 5.6-fold higher contrast-to-noise ratio, and more accurate background noise removal with approximately 2 × improved F1 score. Our approach enhances manual gating and automated phenotyping with cell-scale downstream analyses. Verified by manual annotations, spatial and density analysis for targeted cell groups reveal subtle but significant differences of cell populations in diseased bone marrow. We anticipate that IMC-Denoise will provide similar benefits across mass cytometric applications to more deeply characterize complex tissue microenvironments

An encyclopedia of mouse DNA elements (Mouse ENCODE)

To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome

Rasch Analysis of the Upper-Limb Sub-scale of the STREAM Tool in an Acute Stroke Population

Background – Stroke is a leading cause of disability worldwide. The most common impairment resulting from stroke is upper limb weakness. Objectives - To determine the usefulness and psychometric validity of the upper limb sub-scale of the STREAM in an acute stroke population. Methods: Rasch Analysis, including unidimensionality assumption testing, determining model fit, and analysis of: reliability, residual correlations, & differential item functioning. Results - 125 individuals were assessed using the upper limb sub-scale of the Stroke Rehabilitation Assessment of Movement (STREAM) tool. Rasch analysis suggests the STREAM is a unidimensional measure. However, when scored using the originally proposed method (0-2), or using the response pattern (0-5) neither variant fit the Rasch model (p < 0.05). Although, the reliability was good (Person-Separation Index – 0.847 & 0.903 respectively). Correcting for the disordered thresholds, and thereby producing the new scoring pattern, led to substantial improvement in the overall fit (chi-square probability of fit - 22%), however, the reliability was slightly reduced (PSI – 0.806). Conclusions - The study proposes a new scoring method for the upper limb sub-scale of the STREAM outcome measure in the acute stroke population.Stroke Associatio

Expression Signatures of Metastatic Capacity in a Genetic Mouse Model of Lung Adenocarcinoma

Background: Non-small cell lung cancer (NSCLC) is the foremost cause of cancer-related death in Western countries, which is due partly to the propensity of NSCLC cells to metastasize. The biologic basis for NSCLC metastasis is not well understood. Methodology/Principal Findings: Here we addressed this deficiency by transcriptionally profiling tumors from a genetic mouse model of human lung adenocarcinoma that develops metastatic disease owing to the expression of K-rasG12D and p53R172H. We identified 2,209 genes that were differentially expressed in distant metastases relative to matched lung tumors. Mining of publicly available data bases revealed this expression signature in a subset of NSCLC patients who had a poorer prognosis than those without the signature. Conclusions/Significance: These findings provide evidence that K-rasG12D; p53R172H mice recapitulate features of human NSCLC metastasis and will provide a useful platform on which to study the biologic basis for lung adenocarcinom

A practical drug discovery project at the undergraduate level

A practical drug discovery project for third-year undergraduates is described. No previous knowledge of medicinal chemistry is assumed. Initial lecture-workshops cover the basic principles; then students are asked to improve the profile of a weakly potent, poorly soluble PI3K inhibitor (1). Compound array design, molecular modelling and screening data analysis are followed by laboratory work in which each student, as part of a team, attempts to synthesise at least two target compounds. The project benefits from significant industrial support, including lectures, student mentoring and consumables. The aim is to make the learning experience as close as possible to real-life industrial situations. Forty-eight target compounds have been prepared, the best of which (5b, 5j, 6b and 6ap) improved the potency and aqueous solubility of the lead compound (1) by 100-1000 fold and 10-fold, respectively