Correcting Multiyear Sea Ice Concentration Estimates from Microwave Satellite Observations with Air Temperature, Sea Ice Drift and Dynamic Tie Points

Arctic sea ice cover is a sensitive climate indicator. Due to the warming climate, it has decreased dramatically in the Arctic over the past three decades. Moreover, multiyear ice (MYI), ice which has survived at least one summer, is decreasing at a much higher rate. MYI concentration can be retrieved from microwave remote sensing data. However, the retrieval shows flaws under specific weather conditions. The current thesis is motivated by the need of better estimates of MYI distribution. It introduces three methods to improve/correct the MYI concentration estimates from microwave satellite observations. The first method builds upon the NASA Team algorithm and uses dynamic tie points to compensate the temporal variations of tie points (typical brightness temperatures of each surface type at all the channels). The MYI retrievals in winters (Oct-May) of the years 1989-2012 show that the method with dynamic tie points yields higher estimates than the original method in most years. Both methods show clear declining trends of the MYI area from 1989 to 2012, which is consistent with the sea ice extent minimum. The MYI concentration retrieval with the NASA Team algorithm is most sensitive to the tie points of MYI and FYI at 19 GHz vertical polarized channel. These tie points should be treated with more caution when dynamic tie points are used. The second and third methods are two correction schemes used to account for radiometric anomalies that trigger the erroneous MYI concentration retrievals from microwave satellite observations. The correction based on air temperature is introduced to restore the underestimated MYI concentration under warm conditions. It utilizes the fact that the warm spell in autumn lasts for a few days and replaces the erroneous MYI concentrations with interpolated ones. It is applied to MYI retrievals from the Environment Canada Ice Concentration Extractor (ECICE) using inputs from QuikSCAT and AMSR-E data, acquired over the Arctic in a series of autumn seasons (Sep-Dec) from 2003 to 2008. The correction works well by identifying and correcting the anomalous MYI concentrations. For September of the six years, it introduces over 1.0x105 km2 MYI area, except for 2005. The correction based on ice drift is designed to correct the overestimated MYI concentrations that are impacted by factors such ice deformation, snow wetness and metamorphism. It utilizes ice drift records to constrain the MYI changes within a predicted contour and uses two thresholds of passive microwave radiometric parameters to account for snow wetness and metamorphism. It is applied to the MYI concentration retrievals from ECICE in winters (Oct-May) from 2002 to 2009. Qualitative comparison with Radarsat-1 SAR images and quantitative comparison against results from previous studies show that the correction works well by removing the anomalous high MYI concentrations. On average, the correction reduces 5.2x105 km2 of the estimated MYI area in Arctic except for the April-May time frame, when the reduction is larger as the warmer weather prompts the condition of the anomalous snow radiometric signatures. Both corrections can be used as post-processings to all the microwave-based MYI concentration retrieval algorithms. Due to the regional effect of weather conditions, they could be important in the operational applications. In addition, both corrections take the spatial and temporal continuity of MYI into account, which gives a new insight that instantaneous observations alone of sea ice may lead to ambiguities in determination of partial ice concentrations. This approach may be applicable to the retrieval of other sea ice parameters as well

Epitaxial Mn5Ge3 (100) layer on Ge(100) substrates obtained by flash lamp annealing

Mn5Ge3 thin films have been demonstrated as a promising spin-injector material for germanium-based spintronic devices. So far, Mn5Ge3 has been grown epitaxially only on Ge (111) substrates. In this letter we present the growth of epitaxial Mn5Ge3 films on Ge (100) substrates. The Mn5Ge3 film is synthetized via sub-second solid-state reaction between Mn and Ge upon flash lamp annealing for 20 ms at the ambient pressure. The single crystalline Mn5Ge3 is ferromagnetic with a Curie temperature of 283 K. Both the c-axis of hexagonal Mn5Ge3 and the magnetic easy axis are parallel to the Ge (100) surface. The millisecond-range flash epitaxy provides a new avenue for the fabrication of Ge-based spin-injectors fully compatible with CMOS technology.Comment: 10 pages, 5 figures, submitted to Appl. Phys. Let

A new tracking algorithm for sea ice age distribution estimation

A new algorithm for estimating sea ice age (SIA) distribution based on the Eulerian advection scheme is presented. The advection scheme accounts for the observed divergence or convergence and freezing or melting of sea ice and predicts consequent generation or loss of new ice. The algorithm uses daily gridded sea ice drift and sea ice concentration products from the Ocean and Sea Ice Satellite Application Facility. The major advantage of the new algorithm is the ability to generate individual ice age fractions in each pixel of the output product or, in other words, to provide a frequency distribution of the ice age allowing to apply mean, median, weighted average or other statistical measures. Comparison with the National Snow and Ice Data Center SIA product revealed several improvements of the new SIA maps and time series. First, the application of the Eulerian scheme provides smooth distribution of the ice age parameters and prevents product undersampling which may occur when a Lagrangian tracking approach is used. Second, utilization of the new sea ice drift product void of artifacts from EUMETSAT OSI SAF resulted in more accurate and reliable spatial distribution of ice age fractions. Third, constraining SIA computations by the observed sea ice concentration expectedly led to considerable reduction of multi-year ice (MYI) fractions. MYI concentration is computed as a sum of all MYI fractions and compares well to the MYI products based on passive and active microwave and SAR products

First-Year and Multiyear Sea Ice Incidence Angle Normalization of Dual-Polarized Sentinel-1 SAR Images in the Beaufort Sea

Automatic and visual sea ice classification of SAR imagery is impeded by the incidence angle dependence of backscatter intensities. Knowledge of the angular dependence of different ice types is therefore necessary to account for this effect. While consistent estimates exist for HH polarization for different ice types, they are lacking HV polarization data, especially for multiyear sea ice. Here we investigate the incidence angle dependence of smooth and rough/deformed first-year and multiyear ice of different ages for wintertime dual-polarization Sentinel-1 C-band SAR imagery in the Beaufort Sea. Assuming a linear relationship, this dependence is determined using the difference in incidence angle and backscatter intensities from ascending and descending images of the same area. At cross-polarization rough/deformed first-year sea ice shows the strongest angular dependence with -text{0.11} dB/1{circ } followed by multiyear sea ice with -text{0.07} dB/text{1}{circ }, and old multiyear ice (older than three years) with -text{0.04} dB/text{1}{circ }. The noise floor is found to have a strong impact on smooth first-year ice and estimated slopes are therefore not fully reliable. At co-polarization, we obtained slope values of -0.24, -0.20, -text{0.15}, and -text{0.10} dB/text{1}{circ } for smooth first-year, rough/deformed first-year, multiyear, and old multiyear sea ice, respectively. Furthermore, we show that imperfect noise correction of the first subswath influences the obtained slopes for multiyear sea ice. We demonstrate that incidence angle normalization should not only be applied to co-polarization but should also be considered for cross-polarization images to minimize intra ice type variation in backscatter intensity throughout the entire image swath

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment