Rapid and robust association mapping of expression quantitative trait loci

We applied a simple and efficient two-step method to analyze a family-based association study of gene expression quantitative trait loci (eQTL) in a mixed model framework. This two-step method produces very similar results to the full mixed model method, with our method being significantly faster than the full model. Using the Genetic Analysis Workshop 15 (GAW15) Problem 1 data, we demonstrated the value of data filtering for reducing the number of tests and controlling the number of false positives. Specifically, we showed that removing non-expressed genes by filtering on expression variability effectively reduced the number of tests by nearly 50%. Furthermore, we demonstrated that filtering on genotype counts substantially reduced spurious detection. Finally, we restricted our analysis to the markers and transcripts that were closely located. We found five times more signals in close proximity (cis-) to transcripts than in our genome-wide analysis. Our results suggest that careful pre-filtering and partitioning of data are crucial for controlling false positives and allowing detection of genuine effects in genetic analysis of gene expression

Numerical simulations with a first order BSSN formulation of Einstein's field equations

We present a new fully first order strongly hyperbolic representation of the BSSN formulation of Einstein's equations with optional constraint damping terms. We describe the characteristic fields of the system, discuss its hyperbolicity properties, and present two numerical implementations and simulations: one using finite differences, adaptive mesh refinement and in particular binary black holes, and another one using the discontinuous Galerkin method in spherical symmetry. The results of this paper constitute a first step in an effort to combine the robustness of BSSN evolutions with very high accuracy numerical techniques, such as spectral collocation multi-domain or discontinuous Galerkin methods.Comment: To appear in Physical Review

Effect of combined water drinking test and dark room provocative testing in Caucasian eyes with narrow angles

Purpose: To assess the usefulness of water drinking test and dark room provocative testing (WDT + DRPT) in current clinical practice by evaluating input parameters from Swept-source Optical Coherence Tomography (SS-OCT) images, and to determine if clinical factors like axial length, central endothelial cell count (CECC) and retinal nerve fibre layer thickness (RNFL) thickness are associated with a positive WDT + DRPT. Methods: SS-OCT examination was performed in consecutive subjects presenting as new patients in the outpatient clinic aged > 40 years. If at least one eye met the inclusion criteria (anterior chamber angles <20° and anterior chamber depth < 2.5 mm on SS-OCT), subjects were included in this study and WDT + DRPT was carried out. The eye with the smallest angle was analysed. The difference in parameters between eyes with a positive (≥8 mmHg) and negative (<8 mmHg) increase in intraocular pressure (IOP) after WDT + DRPT were statistically analysed. Second, the correlation between IOP increase after WDT + DRPT and anterior chamber angle parameters (RNFL thickness, CECC and axial length) was studied. Results: A total of 95 subjects with a mean age of 64 years were included. There was an association between IOP increase after WDT + DRPT and anterior chamber angle characteristics, however this was not of clinical significance. No positive results after WDT + DRPT were found in patients with anterior chamber angles ≥ 20°. Conclusions: The present findings indicate that this combined provocative test has no definite correlative or predictive value in angle closure disease. Further, the test is not useful in predicting early diagnosis or possible CECC or RNFL loss

Objective allergy markers and risk of cancer mortality and hospitalization in a large population-based cohort

PURPOSE: There are indications that a history of allergy may offer some protection against cancer. We studied the relation of three objectively determined allergy markers with cancer mortality and hospitalization risk. METHODS: Associations between three allergy markers (number of peripheral blood eosinophil counts, skin test positivity, and serum total IgE) with mortality and hospitalization from any type and four common types of cancer (lung, colorectal, prostate, and breast cancer) were assessed in the Vlagtwedde-Vlaardingen cohort (1965-1990), with follow-up of mortality until 31 December 2008. Hospitalization data were available since 1 January 1995. RESULTS: There were no significant associations between objective allergy markers and cancer mortality or hospitalization. We found several associations in specific subgroups. A higher number of eosinophils was associated with a decreased risk of colorectal cancer mortality in ever smokers HR (95 % CI) = 0.61 (0.45-0.83) and in males 0.59 (0.42-0.83); however, no overall association was observed 0.84 (0.64-1.09). Skin test positivity was associated with a decreased risk of any cancer mortality only among females 0.59 (0.38-0.91) and showed no overall association 0.83 (0.67-1.04). Serum total IgE levels were associated with an increased risk of lung cancer mortality among females 4.64 (1.04-20.70), but with a decreased risk of cancer hospitalization in ever smokers 0.77 (0.61-0.97) and males 0.72 (0.55-0.93); however, no overall associations were observed [mortality 0.99 (0.79-1.25), and hospitalization 0.86 (0.71-1.04)]. CONCLUSIONS: We found no associations between objective allergy markers and cancer in the total population. However, skin test positivity and a high number of eosinophils were associated with a reduced risk to die of cancer in specific subgroups. Hence, it seems important to study specific subgroups defined by gender and smoking habits in order to identify allergy markers of predictive value for cancer mortality

Tumor Vascular Morphology Undergoes Dramatic Changes during Outgrowth of B16 Melanoma While Proangiogenic Gene Expression Remains Unchanged

In established tumors, angiogenic endothelial cells (ECs) coexist next to “quiescent” EC in matured vessels. We hypothesized that angio-gene expression of B16.F10 melanoma would differ depending on the growth stage. Unraveling the spatiotemporal nature thereof is essential for drug regimen design aimed to affect multiple neovascularization stages. We determined the angiogenic phenotype—represented by 52 angio-genes—and vascular morphology of small, intermediate, and large s.c. growing mouse B16.F10 tumors and demonstrated that expression of these genes did not differ between the different growth stages. Yet vascular morphology changed dramatically from small vessels without lumen in small to larger vessels with increased lumen size in intermediate/large tumors. Separate analysis of these vascular morphologies revealed a significant difference in αSMA expression in relation to vessel morphology, while no relation with VEGF, HIF-1α, nor Dll4 expression levels was observed. We conclude that the tumor vasculature remains actively engaged in angiogenesis during B16.F10 melanoma outgrowth and that the major change in tumor vascular morphology does not follow molecular concepts generated in other angiogenesis models

Alkenone Distributions and Hydrogen Isotope Ratios Show Changes in Haptophyte Species and Source Water in the Holocene Baltic Sea

The Baltic Sea, a dynamic, marginal marine basin, experienced a number of large changes in salinity during the Holocene as a result of fluctuations in global and local sea level related to melting of glacial ice sheets and subsequent isostatic rebound. These changes likely had pronounced effects on the species composition of haptophytes, a common phytoplankton group found in the Baltic Sea. This dynamic environment provides the ideal setting to study how species change impacts distribution and hydrogen isotope ratios of long‐chain alkenones (δ²H_(C37)), haptophyte‐specific biomarkers. Here we analyzed the aforementioned parameters in Holocene sediments covering the contrasting hydrological phases of the Baltic Sea. Alkenone distributions changed with different Baltic Sea salinity phases, suggesting that species shifts coincide with salinity change. δ²H_(C37) values show two major shifts: one in the middle of the freshwater Ancylus Lake phase (10.6 to 7.7 ka) and a second at the transition from the brackish Littorina Sea phase (7.2 to 3 ka) into the fresher Modern Baltic (3 ka to the present). The first shift represents a significant enrichment of 50‰, which cannot be explained by salinity or species changes only. At this time, the isotopically depleted ice sheets had melted, and only the relatively enriched freshwater source remained. The second shift, coincident with a change in distribution, is likely caused by a change in species composition alone. These findings show that hydrogen isotope ratios of long‐chain alkenones, combined with their relative distribution, can be used to reconstruct changes in source water