Detection of Ocean Glint and Ozone Absorption Using LCROSS Earth Observations

The Lunar CRater Observation and Sensing Satellite (LCROSS) observed the distant Earth on three occasions in 2009. These data span a range of phase angles, including a rare crescent phase view. For each epoch, the satellite acquired near-infrared and mid-infrared full-disk images, and partial-disk spectra at 0.26-0.65 microns (R~500) and 1.17-2.48 microns (R~50). Spectra show strong absorption features due to water vapor and ozone, which is a biosignature gas. We perform a significant recalibration of the UV-visible spectra and provide the first comparison of high-resolution visible Earth spectra to the NASA Astrobiology Institute's Virtual Planetary Laboratory three-dimensional spectral Earth model. We find good agreement with the observations, reproducing the absolute brightness and dynamic range at all wavelengths for all observation epochs, thus validating the model to within the ~10% data calibration uncertainty. Data-model comparisons reveal a strong ocean glint signature in the crescent phase dataset, which is well matched by our model predictions throughout the observed wavelength range. This provides the first observational test of a technique that could be used to determine exoplanet habitability from disk-integrated observations at visible and near-infrared wavelengths, where the glint signal is strongest. We examine the detection of the ozone 255 nm Hartley and 400-700 nm Chappuis bands. While the Hartley band is the strongest ozone feature in Earth's spectrum, false positives for its detection could exist. Finally, we discuss the implications of these findings for future exoplanet characterization missions.Comment: Accepted to The Astrophysical Journal; recalibration data for LCROSS VSP can be found at: https://sites.google.com/site/tdrobinsonscience/science/moo

GoMiner: a resource for biological interpretation of genomic and proteomic data

We have developed GoMiner, a program package that organizes lists of 'interesting' genes (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. GoMiner provides quantitative and statistical output files and two useful visualizations. The first is a tree-like structure analogous to that in the AmiGO browser and the second is a compact, dynamically interactive 'directed acyclic graph'. Genes displayed in GoMiner are linked to major public bioinformatics resources

Isotropic 3D Nuclear Morphometry of Normal, Fibrocystic and Malignant Breast Epithelial Cells Reveals New Structural Alterations

Grading schemes for breast cancer diagnosis are predominantly based on pathologists' qualitative assessment of altered nuclear structure from 2D brightfield microscopy images. However, cells are three-dimensional (3D) objects with features that are inherently 3D and thus poorly characterized in 2D. Our goal is to quantitatively characterize nuclear structure in 3D, assess its variation with malignancy, and investigate whether such variation correlates with standard nuclear grading criteria.We applied micro-optical computed tomographic imaging and automated 3D nuclear morphometry to quantify and compare morphological variations between human cell lines derived from normal, benign fibrocystic or malignant breast epithelium. To reproduce the appearance and contrast in clinical cytopathology images, we stained cells with hematoxylin and eosin and obtained 3D images of 150 individual stained cells of each cell type at sub-micron, isotropic resolution. Applying volumetric image analyses, we computed 42 3D morphological and textural descriptors of cellular and nuclear structure.We observed four distinct nuclear shape categories, the predominant being a mushroom cap shape. Cell and nuclear volumes increased from normal to fibrocystic to metastatic type, but there was little difference in the volume ratio of nucleus to cytoplasm (N/C ratio) between the lines. Abnormal cell nuclei had more nucleoli, markedly higher density and clumpier chromatin organization compared to normal. Nuclei of non-tumorigenic, fibrocystic cells exhibited larger textural variations than metastatic cell nuclei. At p<0.0025 by ANOVA and Kruskal-Wallis tests, 90% of our computed descriptors statistically differentiated control from abnormal cell populations, but only 69% of these features statistically differentiated the fibrocystic from the metastatic cell populations.Our results provide a new perspective on nuclear structure variations associated with malignancy and point to the value of automated quantitative 3D nuclear morphometry as an objective tool to enable development of sensitive and specific nuclear grade classification in breast cancer diagnosis

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

SummaryWe describe a comprehensive genomic characterization of adrenocortical carcinoma (ACC). Using this dataset, we expand the catalogue of known ACC driver genes to include PRKAR1A, RPL22, TERF2, CCNE1, and NF1. Genome wide DNA copy-number analysis revealed frequent occurrence of massive DNA loss followed by whole-genome doubling (WGD), which was associated with aggressive clinical course, suggesting WGD is a hallmark of disease progression. Corroborating this hypothesis were increased TERT expression, decreased telomere length, and activation of cell-cycle programs. Integrated subtype analysis identified three ACC subtypes with distinct clinical outcome and molecular alterations which could be captured by a 68-CpG probe DNA-methylation signature, proposing a strategy for clinical stratification of patients based on molecular markers

Detection of Ocean Glint and Ozone Absorption Using LCROSS Earth Observations

The Lunar CRater Observation and Sensing Satellite (LCROSS) observed the distant Earth on three occasions in 2009. These data span a range of phase angles, including a rare crescent phase view. For each epoch, the satellite acquired near-infrared and mid-infrared full-disk images, and partial-disk spectra at 0.26-0.65 μm (λ/Δλ ~ 500) and 1.17-2.48 μm (λ/Δλ ~ 50). Spectra show strong absorption features due to water vapor and ozone, which is a biosignature gas. We perform a significant recalibration of the UV-visible spectra and provide the first comparison of high-resolution visible Earth spectra to the NASA Astrobiology Institute's Virtual Planetary Laboratory three-dimensional spectral Earth model. We find good agreement with the observations, reproducing the absolute brightness and dynamic range at all wavelengths for all observation epochs, thus validating the model to within the ~10% data calibration uncertainty. Data-model comparisons reveal a strong ocean glint signature in the crescent phase data set, which is well matched by our model predictions throughout the observed wavelength range. This provides the first observational test of a technique that could be used to determine exoplanet habitability from disk-integrated observations at visible and near-infrared wavelengths, where the glint signal is strongest. We examine the detection of the ozone 255 nm Hartley and 400-700 nm Chappuis bands. While the Hartley band is the strongest ozone feature in Earth's spectrum, false positives for its detection could exist. Finally, we discuss the implications of these findings for future exoplanet characterization missions.This work was performed as part of the NASA Astrobiology Institute’s Virtual Planetary Laboratory, supported by the National Aeronautics and Space Administration through the NASA Astrobiology Institute under solicitation No. NNH05ZDA001C. This research was also supported by the NASA Lunar Science Institute (NLSI) under solicitation No. NNH08ZDA008C, “Scientific and Exploration Potential of the Lunar Poles” (PI: B. Bussey). T.R. gratefully acknowledges support from an appointment to the NASA Postdoctoral Program at the Ames Research Center, administered by Oak Ridge Associated Universities. STScI is operated by the Association for Universities of Research in Astronomy, Inc., under NASA contract NAS5–26555