Surveying drifting icebergs and ice islands: Deterioration detection and mass estimation with aerial photogrammetry and laser scanning

Icebergs and ice islands (large, tabular icebergs) are challenging targets to survey due to their size, mobility, remote locations, and potentially difficult environmental conditions. Here, we assess the precision and utility of aerial photography surveying with structure-from-motion multi-view stereo photogrammetry processing (SfM) and vessel-based terrestrial laser scanning (TLS) for iceberg deterioration detection and mass estimation. For both techniques, we determine the minimum amount of change required to reliably resolve iceberg deterioration, the deterioration detection threshold (DDT), using triplicate surveys of two iceberg survey targets. We also calculate their relative uncertainties for iceberg mass estimation. The quality of deployed Global Positioning System (GPS) units that were used for drift correction and scale assignment was a major determinant of point cloud precision. When dual-frequency GPS receivers were deployed, DDT values of 2.5 and 0.40 m were calculated for the TLS and SfM point clouds, respectively. In contrast, values of 6.6 and 3.4 m were calculated when tracking beacons with lower-quality GPS were used. The SfM dataset was also more precise when used for iceberg mass estimation, and we recommend further development of this technique for iceberg-related end-uses

Pure Stationary States of Open Quantum Systems

Using Liouville space and superoperator formalism we consider pure stationary states of open and dissipative quantum systems. We discuss stationary states of open quantum systems, which coincide with stationary states of closed quantum systems. Open quantum systems with pure stationary states of linear oscillator are suggested. We consider stationary states for the Lindblad equation. We discuss bifurcations of pure stationary states for open quantum systems which are quantum analogs of classical dynamical bifurcations.Comment: 7p., REVTeX

Epigenomic Comparison Reveals Activation of “Seed” Enhancers during Transition from Naive to Primed Pluripotency

SummaryNaive mouse embryonic stem cells (mESCs) and primed epiblast stem cells (mEpiSCs) represent successive snapshots of pluripotency during embryogenesis. Using transcriptomic and epigenomic mapping we show that a small fraction of transcripts are differentially expressed between mESCs and mEpiSCs and that these genes show expected changes in chromatin at their promoters and enhancers. Unexpectedly, the cis-regulatory circuitry of genes that are expressed at identical levels between these cell states also differs dramatically. In mESCs, these genes are associated with dominant proximal enhancers and dormant distal enhancers, which we term seed enhancers. In mEpiSCs, the naive-dominant enhancers are lost, and the seed enhancers take up primary transcriptional control. Seed enhancers have increased sequence conservation and show preferential usage in downstream somatic tissues, often expanding into super enhancers. We propose that seed enhancers ensure proper enhancer utilization and transcriptional fidelity as mammalian cells transition from naive pluripotency to a somatic regulatory program

The relative and absolute timing accuracy of the EPIC-pn camera on XMM-Newton, from X-ray pulsations of the Crab and other pulsars

Reliable timing calibration is essential for the accurate comparison of XMM-Newton light curves with those from other observatories, to ultimately use them to derive precise physical quantities. The XMM-Newton timing calibration is based on pulsar analysis. However, as pulsars show both timing noise and glitches, it is essential to monitor these calibration sources regularly. To this end, the XMM-Newton observatory performs observations twice a year of the Crab pulsar to monitor the absolute timing accuracy of the EPIC-pn camera in the fast Timing and Burst modes. We present the results of this monitoring campaign, comparing XMM-Newton data from the Crab pulsar (PSR B0531+21) with radio measurements. In addition, we use five pulsars (PSR J0537-69, PSR B0540-69, PSR B0833-45, PSR B1509-58 and PSR B1055-52) with periods ranging from 16 ms to 197 ms to verify the relative timing accuracy. We analysed 38 XMM-Newton observations (0.2-12.0 keV) of the Crab taken over the first ten years of the mission and 13 observations from the five complementary pulsars. All the data were processed with the SAS, the XMM-Newton Scientific Analysis Software, version 9.0. Epoch folding techniques coupled with \chi^{2} tests were used to derive relative timing accuracies. The absolute timing accuracy was determined using the Crab data and comparing the time shift between the main X-ray and radio peaks in the phase folded light curves. The relative timing accuracy of XMM-Newton is found to be better than 10^{-8}. The strongest X-ray pulse peak precedes the corresponding radio peak by 306\pm9 \mus, which is in agreement with other high energy observatories such as Chandra, INTEGRAL and RXTE. The derived absolute timing accuracy from our analysis is \pm48 \mus.Comment: 16 pages, 9 figures. Accepted for publication on A&

A model-based approach to selection of tag SNPs

BACKGROUND: Single Nucleotide Polymorphisms (SNPs) are the most common type of polymorphisms found in the human genome. Effective genetic association studies require the identification of sets of tag SNPs that capture as much haplotype information as possible. Tag SNP selection is analogous to the problem of data compression in information theory. According to Shannon's framework, the optimal tag set maximizes the entropy of the tag SNPs subject to constraints on the number of SNPs. This approach requires an appropriate probabilistic model. Compared to simple measures of Linkage Disequilibrium (LD), a good model of haplotype sequences can more accurately account for LD structure. It also provides a machinery for the prediction of tagged SNPs and thereby to assess the performances of tag sets through their ability to predict larger SNP sets. RESULTS: Here, we compute the description code-lengths of SNP data for an array of models and we develop tag SNP selection methods based on these models and the strategy of entropy maximization. Using data sets from the HapMap and ENCODE projects, we show that the hidden Markov model introduced by Li and Stephens outperforms the other models in several aspects: description code-length of SNP data, information content of tag sets, and prediction of tagged SNPs. This is the first use of this model in the context of tag SNP selection. CONCLUSION: Our study provides strong evidence that the tag sets selected by our best method, based on Li and Stephens model, outperform those chosen by several existing methods. The results also suggest that information content evaluated with a good model is more sensitive for assessing the quality of a tagging set than the correct prediction rate of tagged SNPs. Besides, we show that haplotype phase uncertainty has an almost negligible impact on the ability of good tag sets to predict tagged SNPs. This justifies the selection of tag SNPs on the basis of haplotype informativeness, although genotyping studies do not directly assess haplotypes. A software that implements our approach is available

Volatility in the Housing Market: Evidence on Risk and Return in the London Sub-market

The impact of volatility in housing market analysis is reconsidered via examination of the risk-return relationship in the London housing market is examined. In addition to providing the first empirical results for the relationship between risk (as measured by volatility) and returns for this submarket, the analysis offers a more general message to empiricists via a detailed and explicit evaluation of the impact of empirical design decisions upon inferences. In particular, the negative risk-return relationship discussed frequently in the housing market literature is examined and shown to depend upon typically overlooked decisions concerning components of the empirical framework from which statistical inferences are drawn

Sample Reproducibility of Genetic Association Using Different Multimarker TDTs in Genome-Wide Association Studies: Characterization and a New Approach

Multimarker Transmission/Disequilibrium Tests (TDTs) are very robust association tests to population admixture and structure which may be used to identify susceptibility loci in genome-wide association studies. Multimarker TDTs using several markers may increase power by capturing high-degree associations. However, there is also a risk of spurious associations and power reduction due to the increase in degrees of freedom. In this study we show that associations found by tests built on simple null hypotheses are highly reproducible in a second independent data set regardless the number of markers. As a test exhibiting this feature to its maximum, we introduce the multimarker -Groups TDT (), a test which under the hypothesis of no linkage, asymptotically follows a distribution with degree of freedom regardless the number of markers. The statistic requires the division of parental haplotypes into two groups: disease susceptibility and disease protective haplotype groups. We assessed the test behavior by performing an extensive simulation study as well as a real-data study using several data sets of two complex diseases. We show that test is highly efficient and it achieves the highest power among all the tests used, even when the null hypothesis is tested in a second independent data set. Therefore, turns out to be a very promising multimarker TDT to perform genome-wide searches for disease susceptibility loci that may be used as a preprocessing step in the construction of more accurate genetic models to predict individual susceptibility to complex diseases

Population analysis of vitamin D receptor polymorphisms and the role of genetic ancestry in an admixed population

The vitamin D receptor (VDR) is an essential protein related to bone metabolism. Some VDR alleles are differentially distributed among ethnic populations and display variable patterns of linkage disequilibrium (LD). In this study, 200 unrelated Brazilians were genotyped using 21 VDR single nucleotide polymorphisms (SNPs) and 28 ancestry informative markers. The patterns of LD and haplotype distribution were compared among Brazilian and the HapMap populations of African (YRI), European (CEU) and Asian (JPT+CHB) origins. Conditional regression and haplotype-specific analysis were performed using estimates of individual genetic ancestry in Brazilians as a quantitative trait. Similar patterns of LD were observed in the 5′ and 3′ gene regions. However, the frequency distribution of haplotype blocks varied among populations. Conditional regression analysis identified haplotypes associated with European and Amerindian ancestry, but not with the proportion of African ancestry. Individual ancestry estimates were associated with VDR haplotypes. These findings reinforce the need to correct for population stratification when performing genetic association studies in admixed populations

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy