Network-based genome-wide association study of Crohn's disease

Genome-wide association studies (GWAS) have rapidly become a standard method for disease gene discovery. Many recent GWAS indicate that for most disorders, only a few common variants are implicated and the associated SNPs explain only a small fraction of the genetic risk. The current study incorporated gene network information into gene-based analysis of GWAS data for Crohn's disease (CD). The purpose was to develop statistical models to boost the power of identifying disease-associated genes and gene subnetworks by maximizing the use of existing biological knowledge from multiple sources. The results revealed that Markov random field (MRF) based mixture model incorporating direct neighborhood information from a single gene network is not efficient in identifying CD-related genes based on the GWAS data. The incorporation of solely direct neighborhood information might lead to the low efficiency of these models. Alternative MRF models looking beyond direct neighboring information are necessary to be developed in the future for the purpose of this study.^

Network-based analysis of genome-wide scans of natural selection

The genomic era brought by recent advances in the next-generation sequencing technology makes the genome-wide scans of natural selection a reality. Currently, almost all the statistical tests and analytical methods for identifying genes under selection was performed on the individual gene basis. Although these methods have the power of identifying gene subject to strong selection, they have limited power in discovering genes targeted by moderate or weak selection forces, which are crucial for understanding the molecular mechanisms of complex phenotypes and diseases. Recent availability and rapid completeness of many gene network and protein-protein interaction databases accompanying the genomic era open the avenues of exploring the possibility of enhancing the power of discovering genes under natural selection. The aim of the thesis is to explore and develop normal mixture model based methods for leveraging gene network information to enhance the power of natural selection target gene discovery. The results show that the developed statistical method, which combines the posterior log odds of the standard normal mixture model and the Guilt-By-Association score of the gene network in a naïve Bayes framework, has the power to discover moderate/weak selection gene which bridges the genes under strong selection and it helps our understanding the biology under complex diseases and related natural selection phenotypes.^

Benthic foraminiferal stable isotope record from ODP Site 138-849 on the East Pacific Rise

Benthic foraminifer and delta13C data from Site 849, on the west flank of the East Pacific Rise (0°11 'N, 110°31'W; 3851 m), give relatively continuous records of deep Pacific Ocean stable isotope variations between 0 and 5 Ma. The mean sample spacing is 4 k.y. Most analyses are from Cibicides wuellerstorfi, but isotopic offsets relative to Uvigerina peregrina appear roughly constant. Because of its location west of the East Pacific Rise, Site 849 yields a suitable record of mean Pacific Ocean delta13C, which approximates a global oceanic signal. The ~100-k.y.-period climate cycle, which is prevalent in delta18O does not dominate the long-term delta13C record. For delta13C, variations in the ~400- and 41-k.y. periods are more important. Phase lags of delta13C relative to ice volume in the 41- and 23-k.y. bands are consistent with delta13C as a measure of organic biomass. A model-calculated exponential response time of 1-2 k.y. is appropriate for carbon stored in soils and shallow sediments responding to glacial-interglacial climate change. Oceanic delta13C leads ice volume slightly in the 100-k.y. band, and this suggests another process such as changes in continental weathering to modulate mean river delta13C at long periods. The delta13C record from Site 849 diverges from that of Site 677 in the Panama Basin mostly because of decay of 13C-depleted organic carbon in the relatively isolated Panama Basin. North Atlantic to Pacific delta13C differences calculated using published data from Sites 607 and 849 reveal variations in Pliocene deep water within the range of those of the late Quaternary. Maximum delta13C contrast between these sites, which presumably reflects maximum influx of high-delta13C northern source water into the deep North Atlantic Ocean, occurred between 1.3 and 2.1 Ma, well after the initiation of Northern Hemisphere glaciation. Export of high-delta13C North Atlantic Deep Water from the Atlantic to the circumpolar Antarctic, as recorded by published delta13C data from Subantarctic Site 704, appears unrelated to the North Atlantic-Pacific delta13C contrast. To account for this observation, we suggest that deep-water formation in the North Atlantic reflects northern source characteristics, whereas export of this water into the circumpolar Antarctic reflects Southern Hemisphere wind forcing. Neither process appears directly linked to ice-volume variations.

Wetland maps including open water extent dynamics based on ENVISAT ASAR WS for Siberia, 2007 and 2008, links to GeoTIFFs

Wetlands store large amounts of carbon, and depending on their status and type, they release specific amounts of methane gas to the atmosphere. The connection between wetland type and methane emission has been investigated in various studies and utilized in climate change monitoring and modelling. For improved estimation of methane emissions, land surface models require information such as the wetland fraction and its dynamics over large areas. Existing datasets of wetland dynamics present the total amount of wetland (fraction) for each model grid cell, but do not discriminate the different wetland types like permanent lakes, periodically inundated areas or peatlands. Wetland types differently influence methane fluxes and thus their contribution to the total wetland fraction should be quantified. Especially wetlands of permafrost regions are expected to have a strong impact on future climate due to soil thawing. In this study ENIVSAT ASAR Wide Swath data was tested for operational monitoring of the distribution of areas with a long-term SW near 1 (hSW) in northern Russia (SW = degree of saturation with water, 1 = saturated), which is a specific characteristic of peatlands. For the whole northern Russia, areas with hSW were delineated and discriminated from dynamic and open water bodies for the years 2007 and 2008. The area identified with this method amounts to approximately 300,000 km**2 in northern Siberia in 2007. It overlaps with zones of high carbon storage. Comparison with a range of related datasets (static and dynamic) showed that hSW represents not only peatlands but also temporary wetlands associated with post-forest fire conditions in permafrost regions. Annual long-term monitoring of change in boreal and tundra environments is possible with the presented approach. Sentinel-1, the successor of ENVISAT ASAR, will provide data that may allow continuous monitoring of these wetland dynamics in the future complementing global observations of wetland fraction.

Digital surface model, hillshade and Lambertian reflectance model of the rock glaciers Oelgrube and Aeusseres Hochebenkar (Oetztal Alps, Tyrol, Austria)

With full-waveform (FWF) lidar systems becoming increasingly available from different commercial manufacturers, the possibility for extracting physical parameters of the scanned surfaces in an area-wide sense, as addendum to their geometric representation, has risen as well. The mentioned FWF systems digitize the temporal profiles of the transmitted laser pulse and of its backscattered echoes, allowing for a reliable determination of the target distance to the instrument and of physical target quantities by means of radiometric calibration, one of such quantities being the diffuse Lambertian reflectance. The delineation of glaciers is a time-consuming task, commonly performed manually by experts and involving field trips as well as image interpretation of orthophotos, digital terrain models and shaded reliefs. In this study, the diffuse Lambertian reflectance was compared to the glacier outlines mapped by experts. We start the presentation with the workflow for analysis of FWF data, their direct georeferencing and the calculation of the diffuse Lambertian reflectance by radiometric calibration; this workflow is illustrated for a large FWF lidar campaign in the Ötztal Alps (Tyrol, Austria), operated with an Optech ALTM 3100 system. The geometric performance of the presented procedure was evaluated by means of a relative and an absolute accuracy assessment using strip differences and orthophotos, resp. The diffuse Lambertian reflectance was evaluated at two rock glaciers within the mentioned lidar campaign. This feature showed good performance for the delineation of the rock glacier boundaries, especially at their lower parts.

ODP Site 162-980 age model and color reflectance record of sediments from ODP Leg 162 sites

Sediment spectral reflectance measurements were generated aboard the JOIDES Resolution during Ocean Drilling Program Leg 162 shipboard operations. The large size of the raw data set (over 1.3 gigabytes) and limited computer hard disk storage space precluded detailed analysis of the data at sea, although broad band averages were used as aids in developing splices and determining lithologic boundaries. This data report describes the methods used to collect these data and their shipboard and postcruise processing. These initial results provide the basis for further postcruise research.

Age model and Plio-Pleistocene benthic stable oxygen isotope ratios of ODP Site 184-1143 in the Sourh China Sea

Based on benthic foraminiferal delta18O from ODP Site 1143, a 5-Myr astronomical timescale for the West Pacific Plio-Pleistocene was established using an automatic orbital tuning method. The tuned Brunhes/Matuyama paleomagnetic polarity reversal age agrees well with the previously published age of 0.78 Ma. The tuned ages for several planktonic foraminifer bio-events also agree well with published dates, and new ages for some other bio-events in the South China Sea were also estimated. The benthic delta18O from Site 1143 is highly coherent with the Earth's orbit (ETP) both at the obliquity and precession bands for the last 5 Myr, and at the eccentricity band for the last 2 Myr. In general, the 41-kyr cycle was dominant through the Plio-Pleistocene although the 23-kyr cycle was also very strong. The 100-kyr cycle became dominant only during the last 1 Myr. A comparison of the benthic delta18O between the Atlantic (ODP 659) and the East and West Pacific (846 and 1143) reveals that the Atlantic-Pacific benthic oxygen isotope difference ratio (Delta delta18OAtl-Pac) displays an increasing trend in three time intervals: 3.6-2.7 Ma, 2.7-2.1 Ma and 1.5-0.25 Ma. Each of the intervals begins with a rapid negative shift in Delta delta18OAtl-Pac, followed by a long period with an increasing trend, corresponding to the growth of the Northern Hemisphere ice sheet. This means that all three intervals of ice sheet growth in the Northern Hemisphere were accompanied at the beginning by a rapid relative warming of deep water in the Atlantic as compared to that of the Pacific, followed by its gradual relative cooling. This general trend, superimposed on the frequent fluctuations with glacial cycles, should yield insights into the processes leading to the boreal glaciation. Cross-spectral analyses of the Delta delta18OAtl-Pac with the Earth's orbit suggests that after the initiation of Northern Hemisphere glaciation at about 2.5 Ma, obliquity rather than precession had become the dominant force controlling the vertical structure or thermohaline circulation in the paleo-ocean.

Biostratigraphy and Sr isotopic composition of sediments from DSDP Legs 12, 14, 15, 17, 20-22, and 30

We present the data used to construct the Cenozoic and Cretaceous portion of the Phanerozoic curve of seawater 87Sr/86Sr that had been given in summary form by W.H. Burke co-workers. All Cenozoic samples (128) and 22 Cretaceous samples are foram-nannofossil oozes and limestones from DSDP cores distributed among 13 sites in the Atlantic, Pacific and Indian Oceans, and the Caribbean Sea. Non-DSDP Cretaceous samples (126) include limestone, anhydrite and phosphate samples from North America, Europe and Asia. Determination of the 87Sr/86Sr value of seawater at particular times in the past is based on comparison of ratios derived from coeval marine samples from widely separated geographic areas. These samples are characterized by a wide variety of diagenetic and burial histories. The large size and cosmopolitan nature of the data set decreases the likelihood that, among coeval data, systematic error has been introduced by a similar pattern of diagenetic alteration of the ratios. There is good clustering of data points throughout the Cenozoic and Cretaceous curve. The consistency of data is illustrated by Cenozoic and Cretaceous data plots that include a separate symbol for each DSDP site and non-DSDP sample location. More than 98% of the data points are enclosed by upper and lower lines that define a narrow band. For any given time, the correct seawater ratio probably lies within this band. A line drawn within the band represents our estimate of the actual seawater ratio as a function of time. The general configuration of the Cenozoic and Cretaceous curve appears to be strongly influenced by the history of plate interactions and sea-floor spreading. Specific rises and falls in the 87Sr/86Sr of seawater, however, may be caused by a variety of factors such as variation in lithologic composition of the crust exposed to weathering, configuration and topographic relief of continents, volcanic activity, rate of sea-floor spreading, extent of continental inundation by epeiric seas, and variations in both climate and paleooceanographic conditions. Many or all of these factors are probably related to global tectonic processes, yet their combined effect on the temporal variation of seawater 87Sr/86Sr can complicate a direct platetectonic interpretation for portions of the seawater curve.

Age models for ODP Leg 172 sites

Ten ODP sites drilled in a depth transect (2164-4775 m water depth) during Leg 172 recovered high-deposition rate (>20 cm/kyr) sedimentary sections from sediment drifts in the western North Atlantic. For each site an age model covering the past 0.8-0.9 Ma has been developed. The time scales have a resolution of 10-20 kyr and are derived by tuning variations of estimated carbonate content to the orbital parameters precession and obliquity. Based on the similarity in the signature of proxy records and the spectral character of the time series, the sites are divided into two groups: precession cycles are better developed in carbonate records from a group of shallow sites (2164-2975 m water depth, Sites 1055-1058) while the deeper sites (2995-4775 m water depth, Sites 1060-1063) are characterized by higher spectral density in the obliquity band. The resulting time scales show excellent coherence with other dated carbonate and isotope records from low latitudes. Besides the typical Milankovitch cyclicity significant variance of the resulting carbonate time series is concentrated at millennial-scale changes with periods of about 12, 6, 4, 2.5, and 1.5 kyr. Comparisons of carbonate records from the Blake Bahama Outer Ridge and the Bermuda Rise reveal a remarkable similarity in the time and frequency domain indicating a basin-wide uniform sedimentation pattern during the last 0.9 Ma.

Age model, stable isotopes, major element proportions and endmember unmixing results from four western tropical Atlantic cores

We investigate changes in the delivery and oceanic transport of Amazon sediments related to terrestrial climate variations over the last 250 ka. We present high-resolution geochemical records from four marine sediment cores located between 5 and 12° N along the northern South American margin. The Amazon River is the sole source of terrigenous material for sites at 5 and 9° N, while the core at 12° N receives a mixture of Amazon and Orinoco detrital particles. Using an endmember unmixing model, we estimated the relative proportions of Amazon Andean material ("%-Andes", at 5 and 9° N) and of Amazon material ("%-Amazon", at 12° N) within the terrigenous fraction. The %-Andes and %-Amazon records exhibit significant precessional variations over the last 250 ka that are more pronounced during interglacials in comparison to glacial periods. High %-Andes values observed during periods of high austral summer insolation reflect the increased delivery of suspended sediments by Andean tributaries and enhanced Amazonian precipitation, in agreement with western Amazonian speleothem records. Increased Amazonian rainfall reflects the intensification of the South American monsoon in response to enhanced land-ocean thermal gradient and moisture convergence. However, low %-Amazon values obtained at 12° N during the same periods seem to contradict the increased delivery of Amazon sediments. We propose that reorganizations in surface ocean currents modulate the northwestward transport of Amazon material. In agreement with published records, the seasonal North Brazil Current retroflection is intensified (or prolonged in duration) during cold substages of the last 250 ka (which correspond to intervals of high DJF or low JJA insolation) and deflects eastward the Amazon sediment and freshwater plume.

Topographic model of Greenland (elevation lines in PanMap and ASCII format)

In this paper, a new high-resolution elevation model of Greenland, including the ice sheet as well as the ice free regions, is presented. It is the first published full coverage model, computed with an average resolution of 2 km and providing an unprecedented degree of detail. The topography is modeled from a wide selection of data sources, including satellite radar altimetry from Geosat and ERS 1, airborne radar altimetry and airborne laser altimetry over the ice sheet, and photogrammetric and manual map scannings in the ice free region. The ice sheet model accuracy is evaluated by omitting airborne laser data from the analysis and treating them as ground truth observations. The mean accuracy of the ice sheet elevations is estimated to be 12-13 m, and it is found that on surfaces of a slope between 0.2° and 0.8°, corresponding to approximately 50% of the ice sheet, the model presents a 40% improvement over models based on satellite altimetry alone. On coastal bedrock, the model is compared with stereo triangulated reference points, and it is found that the model accuracy is of the order of 25-35 m in areas covered by stereo photogrammetry scannings and between 200 and 250 m elsewhere.

The VLT/NaCo large program to probe the occurrence of exoplanets and brown dwarfs at wide orbits II. Survey description, results, and performances

Context. Young, nearby stars are ideal targets for direct imaging searches for giant planets and brown dwarf companions. After the first-imaged planet discoveries, vast efforts have been devoted to the statistical analysis of the occurence and orbital distributions of giant planets and brown dwarf companions at wide (>= 5-6 AU) orbits. Aims. In anticipation of the VLT/SPHERE planet-imager, guaranteed-time programs, we have conducted a preparatory survey of 86 stars between 2009 and 2013 to identify new faint comoving companions to ultimately analyze the occurence of giant planets and brown dwarf companions at wide (10-2000 AU) orbits around young, solar-type stars. Methods. We used NaCo at VLT to explore the occurrence rate of giant planets and brown dwarfs between typically 0.1 and 8 ''. Diffraction-limited observations in H-band combined with angular differential imaging enabled us to reach primary star-companion brightness ratios as small as 10(-6) at 1.5 ''. Repeated observations at several epochs enabled us to discriminate comoving companions from background objects. Results. During our survey, twelve systems were resolved as new binaries, including the discovery of a new white dwarf companion to the star HD8049. Around 34 stars, at least one companion candidate was detected in the observed field of view. More than 400 faint sources were detected; 90% of them were in four crowded fields. With the exception of HD8049 B, we did not identify any new comoving companions. The survey also led to spatially resolved images of the thin debris disk around HD61005 that have been published earlier. Finally, considering the survey detection limits, we derive a preliminary upper limit on the frequency of giant planets for the semi-major axes of [10, 2000] AU: typically less than 15% between 100 and 500 AU and less than 10% between 50 and 500 AU for exoplanets that are more massive than 5 M-Jup and 10 M-Jup respectively, if we consider a uniform input distribution and a confidence level of 95%. Conclusions. The results from this survey agree with earlier programs emphasizing that massive, gas giant companions on wide orbits around solar-type stars are rare. These results will be part of a broader analysis of a total of similar to 210 young, solar-type stars to bring further statistical constraints for theoretical models of planetary formation and evolution.