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  • 1
    Publication Date: 2016-12-19
    Type: Conference or Workshop Item , NonPeerReviewed
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  • 2
    Publication Date: 2018-05-07
    Description: In order to describe texture and microstructure of a polycrystalline material completely, crystal orientation g={?1F?2} must be known in all points x={x1?x2?x3} of the material. This can be achieved by locationresolved diffraction of high-energy, i.e. short-wave, X-rays from synchrotron sources. Highest resolution in the orientation- as well as the location-coordinates can be achieved by three variants of a detector sweeping technique in which an area detector is continuously moved during exposure. This technique results in two-dimensionally continuous images which are sections and projections of the six-dimensional orientation location space. Further evaluation of these images depends on whether individual grains are resolved in them or not. Because of the high penetration depth of high-energy synchrotron radiation in matter, this technique is also, and particularly, suitable for the investigation of the interior of big samples.
    Keywords: VAE 120 ; VKA 200 ; VGA 410 ; 38.03
    Language: English
    Type: article , publishedVersion
    Format: application/pdf
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  • 3
    Publication Date: 2019-07-13
    Description: Aerosols have important impacts on air quality and climate, but the processes affecting their removal from the atmosphere are not fully understood and are poorly constrained by observations. This makes modelled aerosol lifetimes uncertain. In this study, we make use of an observational constraint on aerosol lifetimes provided by radionuclide measurements and investigate the causes of differences within a set of global models. During the Fukushima Dai-Ichi nuclear power plant accident of March 2011, the radioactive isotopes cesium-137 (Cs-137) and xenon-133 (Xe-133) were released in large quantities. Cesium attached to particles in the ambient air, approximately according to their available aerosol surface area. Cs-137 size distribution measurements taken close to the power plant suggested that accumulation mode (AM) sulfate aerosols were the main carriers of cesium. Hence, Cs-137 can be used as a proxy tracer for the AM sulfate aerosol's fate in the atmosphere. In contrast, the noble gas Xe-133 behaves almost like a passive transport tracer. Global surface measurements of the two radioactive isotopes taken over several months after the release allow the derivation of a lifetime of the carrier aerosol. We compare this to the lifetimes simulated by 19 different atmospheric transport models initialized with identical emissions of Cs-137that were assigned to an aerosol tracer with each model's default properties of AM sulfate, and Xe-133 emissions that were assigned to a passive tracer. We investigate to what extent the modelled sulfate tracer can reproduce the measurements, especially with respect to the observed loss of aerosol mass with time. Modelled Cs-137and Xe-133 concentrations sampled at the same location and times as station measurements allow a direct comparison between measured and modelled aerosol lifetime. The e-folding lifetime e, calculated from station measurement data taken between 2 and 9 weeks after the start of the emissions, is 14.3 days (95% confidence interval 13.1-15.7 days). The equivalent modelled e lifetimes have a large spread, varying between 4.8 and 26.7 days with a model median of 9.42.3 days, indicating too fast a removal in most models. Because sufficient measurement data were only available from about 2 weeks after the release, the estimated lifetimes apply to aerosols that have undergone long-range transport, i.e. not for freshly emitted aerosol. However, modelled instantaneous lifetimes show that the initial removal in the first 2 weeks was quicker (lifetimes between 1 and 5 days) due to the emissions occurring at low altitudes and co-location of the fresh plume with strong precipitation. Deviations between measured and modelled aerosol lifetimes are largest for the northernmost stations and at later time periods, suggesting that models do not transport enough of the aerosol towards the Arctic. The models underestimate passive tracer (Xe-133) concentrations in the Arctic as well but to a smaller extent than for the aerosol (Cs-137) tracer. This indicates that in addition to too fast an aerosol removal in the models, errors in simulated atmospheric transport towards the Arctic in most models also contribute to the underestimation of the Arctic aerosol concentrations.
    Keywords: Meteorology and Climatology
    Type: GSFC-E-DAA-TN30865 , Atmospheric Chemistry and Physics; 16; 5; 3525-3561
    Format: text
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  • 4
    Publication Date: 2016-09-17
    Description: In the biology of tissue development and diseases, DNA methylation plays an important role. For a deeper understanding, it is crucial to accurately compare DNA methylation patterns between groups of samples representing different conditions. A widely used method to investigate DNA methylation in the CpG context is bisulfite sequencing, which produces data on the single-nucleotide scale. While there are benefits to analyzing CpG sites on a basepair level, there are both biological and statistical reasons to test entire genomic regions for differential methylation. However, the analysis of DNA methylation is hampered by the lack of best practice standards. Here, we compared multiple approaches for testing predefined genomic regions for differential DNA methylation in bisulfite sequencing data. Nine methods were evaluated: BiSeq, COHCAP, Goeman's Global Test, Limma, methylKit/eDMR, RADMeth and three log-linear regression approaches with different distribution assumptions. We applied these methods to simulated data and determined their sensitivity and specificity. This revealed performance differences, which were also seen when applied to real data. Methods that first test single CpG sites and then test regions based on transformed CpG-wise P -values performed better than methods that summarize methylation levels or raw reads. Interestingly, smoothing of methylation levels had a negligible impact. In particular, Global Test, BiSeq and RADMeth/ z -test outperformed the other methods we evaluated, providing valuable guidance for more accurate analysis of DNA methylation.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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  • 5
    Publication Date: 2017-08-01
    Description: The Community Atmosphere Model (CAM) adopts Cloud Layers Unified By Binormals scheme (CLUBB) and an updated microphysics (MG2) scheme for a more unified treatment of cloud processes. This makes interactions between parameterizations tighter and more explicit. In this study, a cloudy planetary boundary layer (PBL) oscillation related to interaction between CLUBB and MG2 is identified in CAM. This highlights the need for consistency between the coupled sub-grid processes in climate model development. This oscillation occurs most often in the marine cumulus cloud regime. The oscillation occurs only if the modeled PBL is strongly decoupled and precipitation evaporates below the cloud. Two aspects of the parameterized coupling assumptions between CLUBB and MG2 schemes cause the oscillation: 1) a parameterized relationship between rain evaporation and CLUBB's sub-grid spatial variance of moisture and heat that induces an extra cooling in the lower PBL; and 2) rain evaporation which happens at a too low an altitude because of the precipitation fraction parameterization in MG2. Either one of these two conditions can overly stabilize the PBL and reduce the upward moisture transport to the cloud layer so that the PBL collapses. Global simulations prove that turning off the evaporation-variance coupling and improving the precipitation fraction parameterization effectively reduces the cloudy PBL oscillation in marine cumulus clouds. By evaluating the causes of the oscillation in CAM, we have identified the PBL processes that should be examined in models having similar oscillations. This study may draw the attention of the modeling and observational communities to the issue of coupling between parameterized physical processes.
    Electronic ISSN: 1942-2466
    Topics: Geography , Geosciences
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
    Publication Date: 2016-06-21
    Description: To assess marine boundary layer (MBL) cloud simulations in three versions of the Community Atmosphere Model (CAM), three sets of short-term global hindcasts are performed and compared to Atmospheric Radiation Measurement (ARM) program observations on Graciosa Island in the Azores from June 2009 to December 2010. The three versions consist of CAM5.3 with default schemes (CAM5.3), CAM5.3 with Cloud Layers Unified By Binormals (CLUBB-MG1), and CAM5.3 with CLUBB and updated microphysics scheme (CLUBB-MG2). Our results show that relative to CAM5.3 default schemes, simulations with CLUBB better represent MBL cloud-base height, the height of the major cloud layer, and the daily cloud cover variability. CLUBB also better simulates the relationship of cloud fraction to cloud liquid water path (LWP) most likely due to CLUBB's consistent treatment of these variables through a probability distribution function (PDF) approach. Sub-cloud evaporation of precipitation is substantially enhanced in simulations with CLUBB-MG2 and is more realistic based on the limited observational estimate. Despite these improvements, all model versions underestimate MBL cloud cover. CLUBB-MG2 reduces biases in in-cloud LWP (clouds are not too bright) but there are still too few of MBL clouds due to an underestimate in the frequency of overcast scenes. Thus combining CLUBB with MG2 scheme better simulates MBL cloud processes, but because biases remain in MBL cloud cover CLUBB-MG2 does not improve the simulation of the surface shortwave cloud radiative effect ( CRE SW ).
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 7
    Publication Date: 2016-01-09
    Description: Notch signaling has recently emerged as an important regulator of immune responses in autoimmune diseases. The recombination signal-binding protein for immunoglobulin kappa J region (RBPJ) is a transcriptional repressor, but converts into a transcriptional activator upon activation of the canonical Notch pathway. Genome-wide association studies of rheumatoid arthritis (RA) identified a susceptibility locus, rs874040 CC , which implicated the RBPJ gene. Here, chromatin state mapping generated using the chromHMM algorithm reveals strong enhancer regions containing DNase I hypersensitive sites overlapping the rs874040 linkage disequilibrium block in human memory, but not in naïve CD4 + T cells. The rs874040 overlapping this chromatin state was associated with increased RBPJ expression in stimulated memory CD4 + T cells from healthy subjects homozygous for the risk allele (CC) compared with memory CD4 + T cells bearing the protective allele (GG). Transcriptomic analysis of rs874040 CC memory T cells showed a repression of canonical Notch target genes IL (interleukin)-9, IL-17 and interferon (IFN) in the basal state. Interestingly, activation of the Notch pathway using soluble Notch ligand, Jagged2-Fc, induced IL-9 and IL-17A while delta-like 4Fc, another Notch ligand, induced higher IFN expression in the rs874040 CC memory CD4 + T cells compared with their rs874040 GG counterparts. In RA, RBPJ expression is elevated in memory T cells from RA patients compared with control subjects, and this was associated with induced inflammatory cytokines IL-9, IL-17A and IFN in response to Notch ligation in vitro . These findings demonstrate that the rs874040 CC allele skews memory T cells toward a pro-inflammatory phenotype involving Notch signaling, thus increasing the susceptibility to develop RA.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 8
    Publication Date: 2015-12-18
    Description: The Ørsted Dal Member of the Upper Triassic Fleming Fjord Formation in East Greenland is well known for its rich vertebrate fauna, represented by numerous specimens of both body and ichnofossils. In particular, the footprints of theropod dinosaurs have been described. Recently, an international expedition discovered several slabs with 100 small chirotheriid pes and manus imprints (pes length 4–4.5 cm) in siliciclastic deposits of this unit. They show strong similarities with Brachychirotherium , a characteristic Upper Triassic ichnogenus with a global distribution. A peculiar feature in the Fleming Fjord specimens is the lack of a fifth digit, even in more deeply impressed imprints. Therefore, the specimens are assigned here tentatively to cf. Brachychirotherium . Possibly, this characteristic is related to the extremely small size and early ontogenetic stage of the trackmaker. The record from Greenland is the first evidence of this morphotype from the Fleming Fjord Formation. Candidate trackmakers are crocodylian stem group archosaurs; however, a distinct correlation with known osteological taxa from this unit is not currently possible. While the occurrence of sauropodomorph plateosaurs in the bone record links the Greenland assemblage more closer to that from the Germanic Basin of central Europe, here the described footprints suggest a Pangaea-wide exchange. Supplementary material: Three-dimensional model of cf. Brachychirotherium pes–manus set (from MGUH 31233b) from the Upper Triassic Fleming Fjord Formation (Norian–Rhaetian) of East Greenland as pdf, ply and jpg files (3D model created by Oliver Wings; photographs taken by Jesper Milàn) is available at https://doi.org/10.6084/m9.figshare.c.2133546
    Print ISSN: 0305-8719
    Electronic ISSN: 2041-4927
    Topics: Geosciences
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  • 9
    Publication Date: 2018-03-06
    Description: Many numerical weather prediction and climate models exhibit too warm lower tropospheres near the mid-latitude continents. The warm bias has been shown to coincide with important surface radiation biases that likely play a critical role in the inception or the growth of the warm bias. This paper presents an attribution study on the net radiation biases in 9 model simulations, performed in the framework of the CAUSES project (Clouds Above the United States and Errors at the Surface). Contributions from deficiencies in the surface properties, clouds, water vapor and aerosols are quantified, using an array of radiation measurement stations near the ARM SGP site. Furthermore, an in-depth analysis is shown to attribute the radiation errors to specific cloud regimes. The net surface shortwave radiation is overestimated in all models throughout most of the simulation period. Cloud errors are shown to contribute most to this overestimation, although non-negligible contributions from the surface albedo exist in most models. Missing deep cloud events and/or simulating deep clouds with too weak cloud-radiative effects dominate in the cloud-related radiation errors. Some models have compensating errors between excessive occurrence of deep cloud, but largely underestimating their radiative effect, while other models miss deep cloud events altogether. Surprisingly, even the latter models tend to produce too much and too frequent afternoon surface precipitation. This suggests that rather than issues with the triggering of deep convection, cloud-radiative deficiencies are related to too weak convective cloud detrainment and too large precipitation efficiencies.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 10
    Publication Date: 2018-11-07
    Description: Forward genetics remains a powerful method for revealing the genes underpinning organismal form and function, and for revealing how these genes are tied together in gene networks. In maize, forward genetics has been tremendously successful, but the size and complexity of the maize genome made identifying mutant genes an often arduous process with traditional methods. The next generation sequencing revolution has allowed for the gene cloning process to be significantly accelerated in many organisms, even when genomes are large and complex. Here, we describe a bulked-segregant analysis sequencing (BSA-Seq) protocol for cloning mutant genes in maize. Our simple strategy can be used to quickly identify a mapping interval and candidate single nucleotide polymorphisms (SNPs) from whole genome sequencing of pooled F2 individuals. We employed this strategy to identify narrow odd dwarf as an enhancer of teosinte branched1 , and to identify a new allele of defective kernel1 . Our method provides a quick, simple way to clone genes in maize.
    Electronic ISSN: 2160-1836
    Topics: Biology
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