Proglacial icings as indicators of glacier thermal regime : ice thickness changes and icing occurrence in Svalbard

Proglacial icings (also known as naled or aufeis) are frequently observed in the forefields of polar glaciers. Their formation has been ascribed to the refreezing of upwelling groundwater that has originated from subglacial melt, and thus the presence of icings has been used as evidence of polythermal glacier regime. We provide an updated analysis of icing occurrence in Svalbard and test the utility of icings as an indicator of thermal regime by comparing icing presence with: (1) mean glacier thickness, as a proxy for present thermal regime; and (2) evidence of past surge activity, which is an indicator of past thermal regime. A total of 279 icings were identified from TopoSvalbard imagery covering the period 2008-2012, of which 143 corresponded to icings identified by Bukowska-Jania and Szafraniec (2005) from aerial photographs from 1990. Only 46% of icings observed in 2008-2012 were found to occur at glaciers with thicknesses consistent with a polythermal regime, meaning a large proportion were associated with glaciers predicted to be of a cold or transitional thermal regime. As a result, icing presence alone may be an unsuitable indicator of glacier regime. We further found that, of the 279 glaciers with icings, 63% of cold-based glaciers and 64% of transitional glaciers were associated with evidence of surge activity. We therefore suggest that proglacial icing formation in Svalbard may reflect historical (rather than present) thermal regime, and that icings possibly originate from groundwater effusion from subglacial taliks that persist for decades following glacier thinning and associated regime change

Copynumber: Efficient algorithms for single- and multi-track copy number segmentation.

BACKGROUND: Cancer progression is associated with genomic instability and an accumulation of gains and losses of DNA. The growing variety of tools for measuring genomic copy numbers, including various types of array-CGH, SNP arrays and high-throughput sequencing, calls for a coherent framework offering unified and consistent handling of single- and multi-track segmentation problems. In addition, there is a demand for highly computationally efficient segmentation algorithms, due to the emergence of very high density scans of copy number. RESULTS: A comprehensive Bioconductor package for copy number analysis is presented. The package offers a unified framework for single sample, multi-sample and multi-track segmentation and is based on statistically sound penalized least squares principles. Conditional on the number of breakpoints, the estimates are optimal in the least squares sense. A novel and computationally highly efficient algorithm is proposed that utilizes vector-based operations in R. Three case studies are presented. CONCLUSIONS: The R package copynumber is a software suite for segmentation of single- and multi-track copy number data using algorithms based on coherent least squares principles.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

High levels of genomic aberrations in serous ovarian cancers are associated with better survival

Martin K Oehler is a member of the Australian Ovarian Cancer Study GroupGenomic instability and copy number alterations in cancer are generally associated with poor prognosis; however, recent studies have suggested that extreme levels of genomic aberrations may be beneficial for the survival outcome for patients with specific tumour types. We investigated the extent of genomic instability in predominantly high-grade serous ovarian cancers (SOC) using two independent datasets, generated in Norway (n = 74) and Australia (n = 70), respectively. Genomic instability was quantified by the Total Aberration Index (TAI), a measure of the abundance and genomic size of copy number changes in a tumour. In the Norwegian cohort, patients with TAI above the median revealed significantly prolonged overall survival (p<0.001) and progression-free survival (p<0.05). In the Australian cohort, patients with above median TAI showed prolonged overall survival (p<0.05) and moderately, but not significantly, prolonged progression-free survival. Results were confirmed by univariate and multivariate Cox regression analyses with TAI as a continuous variable. Our results provide further evidence supporting an association between high level of genomic instability and prolonged survival of high-grade SOC patients, possibly as disturbed genome integrity may lead to increased sensitivity to chemotherapeutic agents.Lars O. Baumbusch, Åslaug Helland, Yun Wang, Knut Liestøl, Marci E. Schaner, Ruth Holm, Dariush Etemadmoghadam, Kathryn Alsop, Pat Brown, Australian Ovarian Cancer Study Group, Gillian Mitchell, Sian Fereday, Anna DeFazio, David D. L. Bowtell, Gunnar B. Kristensen, Ole Christian Lingjærde, Anne-Lise Børresen-Dal

BIOINFORMATICS APPLICATIONS NOTE Genetics and population analysis CGH-Explorer: a program for analysis of array-CGH data

Summary: CGH-Explorer is a program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion. Availability: The program is available as Java class files that runs on any platform with the Java 2 runtime environment (J2SE JRE) installed, and as a Windows executable. Java source files are als

Simulating snow redistribution and its effect on ground surface temperature at a high‐Arctic site on Svalbard

In high‐latitude and mountain regions, local processes such as redistribution by wind, snow metamorphism and percolation of water, produce a complex spatial distribution of snow depths and snow densities. With its strong control on the ground thermal regime, this snow distribution has pronounced effects on ground temperatures at small spatial scales which are typically not resolved by land surface models (LSMs). This limits our ability to simulate the local impacts of climate change on for example vegetation and permafrost. Here, we present a tiling approach combining the CryoGrid permafrost model with snow microphysics parametrizations from the CROCUS snow scheme to account for sub‐grid lateral exchange of snow and water in a process‐based way. We demonstrate that a simple setup with three coupled tiles, each representing a different snow accumulation class with a specific topographic setting, can reproduce the observed spread of winter‐time ground surface temperatures (GST) and end‐of‐season snow distribution for a high‐Arctic site on Svalbard. For the three‐year study period, the three‐tile simulations showed substantial improvement compared to traditional single‐tile simulations which naturally cannot account for sub‐grid variability. Amongst others, the representation of the warmest and coldest 5% of the observed GST distribution was improved by 1‐2°C, while still capturing the average of the distribution. The simulations also reveal positive mean annual GSTs at the locations receiving the greatest snow cover. This could be an indication for the onset of localized permafrost degradation which would be obscured in single‐tile simulations