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  • 1
    Publication Date: 2016-07-08
    Description: Despite the fact that squab is consumed throughout the world because of its high nutritional value and appreciated sensory attributes, aspects related to its characterization, and in particular genetic issues, have rarely been studied. In this study, meat traits in terms of pH, water-holding capacity, intramuscular fat content, and fatty acid profile of the breast muscle of squabs from two meat pigeon breeds were determined. Breed-specific differences were detected in fat-related traits of intramuscular fat content and fatty acid composition. RNA-Sequencing was applied to compare the transcriptomes of muscle and liver tissues between squabs of two breeds to identify candidate genes associated with the differences in the capacity of fat deposition. A total of 27 differentially expressed genes assigned to pathways of lipid metabolism were identified, of which, six genes belonged to the peroxisome proliferator-activated receptor signaling pathway along with four other genes. Our results confirmed in part previous reports in livestock and provided also a number of genes which had not been related to fat deposition so far. These genes can serve as a basis for further investigations to screen markers closely associated with intramuscular fat content and fatty acid composition in squabs. The data from this study were deposited in the National Center for Biotechnology Information (NCBI)’s Sequence Read Archive under the accession numbers SRX1680021 and SRX1680022. This is the first transcriptome analysis of the muscle and liver tissue in Columba using next generation sequencing technology. Data provided here are of potential value to dissect functional genes influencing fat deposition in squabs.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 2
    Publication Date: 2015-12-01
    Description: We present a detailed investigation on the doping dependence of the upper critical field H c 2 ( T ) of FeSe x Te 1− x thin films (0.18 ≤  x  ≤ 0.90) by measuring the electrical resistivity as a function of magnetic field. The H c 2 ( T ) curves exhibit a downturn behavior with decreasing temperature in all the samples, owing to the Pauli-limited effect (spin paramagnetic effect). The Pauli-limited effect on the upper critical field can be monotonically modulated by variation of the Se/Te composition. Our results show that Te-doping induced disorder and excess Fe atoms give rise to enhancement of the Pauli-limited effect.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
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  • 3
    Publication Date: 2015-03-11
    Description: We present the adjoint of a cirrus formation parameterization that computes the sensitivity of ice crystal number concentration to updraft velocity, aerosol, and ice deposition coefficient. The adjoint is driven by simulations from the NCAR Community Atmosphere Model Version 5.1 to understand the sensitivity of formed ice crystal number concentration to 13 variables and quantify which contribute to its variability. Sensitivities of formed ice crystal number concentration to updraft velocity, sulfate number, and sulfate diameter are positive and largest over the coldest regions of the globe. Sulfate number sensitivity is also large over the tropics where updraft cooling is sufficient but sulfate number concentration is low, indicating a sulfate-limited regime in CAM 5.1. Outside of the tropics, competition between homogeneous and heterogeneous nucleation may shift annually-averaged sensitivities to higher magnitudes, when infrequent strong updrafts shift crystal production away from purely heterogeneous nucleation. Outside the tropics, updraft velocity is responsible for approximately 52.70% of the ice crystal number variability. In the tropics, sulfate number concentration and updraft jointly control variability in formed crystal number concentration. Insoluble aerosol species play a secondary, but still important, role in influencing the variability in crystal concentrations, with coarse mode dust being the largest contributor at nearly 50% in certain regions. On a global scale, more than 95% of the temporal variability in crystal number concentration can be described by temperature, updraft velocity, sulfate number, and coarse mode dust number concentration.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
    Publication Date: 2011-08-03
    Description: Sonic hedgehog (Shh) signaling plays diverse roles during animal development and adult tissue homeostasis through differential regulation of Gli family transcription factors. Dysregulated Shh signaling activities have been linked to birth defects and tumorigenesis. Here we report that Brg, an ATP-dependent chromatin remodeling factor, has dual functions in regulating Shh target gene expression. Using a Brg conditional deletion in Shh-responding neural progenitors and fibroblasts, we demonstrate that Brg is required both for repression of the basal expression and for the activation of signal-induced transcription of Shh target genes. In developing telencephalons deficient for Brg, Shh target genes were derepressed, whereas Brg-deleted cerebellar granule neuron precursors failed to respond to Shh to increase their proliferation. The repressor function of Brg was mediated through Gli3 and both the repressor and activator functions of Brg appeared to be independent of its ATPase activity. Furthermore, Brg facilitates Gli coactivator histone deacetylase (HDAC) binding to the regulatory regions of Shh target genes, providing a possible mechanism for its positive role in Shh signaling. Our results thus reveal that a complex chromatin regulation mechanism underlies the precise transcription outcomes of Shh signaling and its diverse roles during development.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 5
    Publication Date: 2013-07-06
    Description: Motivation: Due to the high complexity of metabolome, the comprehensive 2D gas chromatography time-of-flight mass spectrometry (GC x GC-TOF MS) is considered as a powerful analytical platform for metabolomics study. However, the applications of GC x GC-TOF MS in metabolomics are not popular owing to the lack of bioinformatics system for data analysis. Results: We developed a computational platform entitled metabolomics profiling pipeline (MetPP) for analysis of metabolomics data acquired on a GC x GC-TOF MS system. MetPP can process peak filtering and merging, retention index matching, peak list alignment, normalization, statistical significance tests and pattern recognition, using the peak lists deconvoluted from the instrument data as its input. The performance of MetPP software was tested with two sets of experimental data acquired in a spike-in experiment and a biomarker discovery experiment, respectively. MetPP not only correctly aligned the spiked-in metabolite standards from the experimental data, but also correctly recognized their concentration difference between sample groups. For analysis of the biomarker discovery data, 15 metabolites were recognized with significant concentration difference between the sample groups and these results agree with the literature results of histological analysis, demonstrating the effectiveness of applying MetPP software for disease biomarker discovery. Availability: The source code of MetPP is available at http://metaopen.sourceforge.net Contact: xiang.zhang@louisville.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 6
    Publication Date: 2013-05-02
    Description: [1]  Single column models (SCM) are useful testbeds for investigating the parameterisation schemes of numerical weather prediction and climate models. The usefulness of SCM simulations are limited, however, by the accuracy of the best-estimate large-scale observations prescribed. Errors estimating the observations will result in uncertainty in modelled simulations. One method to address the modelled uncertainty is to simulate an ensemble where the ensemble members span observational uncertainty. This study first derives an ensemble of large-scale data for the Tropical Warm Pool International Cloud Experiment (TWP-ICE) based on an estimate of a possible source of error in the best-estimate product. This data is then used to carry out simulations with 11SCM and 2 cloud-resolving models (CRM). Best-estimate simulations are also performed. All models show that moisture-related variables are close to observations and there are limited differences between the best-estimate and ensemble mean values. The models, however, show different sensitivities to changes in the forcing particularly when weakly forced. The ensemble simulations highlight important differences in the surface evaporation term of the moisture budget between the SCM and CRM. Differences are also apparent between the models in the ensemble mean vertical structure of cloud variables whilst for each model cloud properties are relatively insensitive to forcing. The ensemble is further used to investigate cloud variables and precipitation and identifies differences between CRM and SCM particularly for relationships involving ice. This study highlights the additional analysis that can be performed using ensemble simulations and hence enables a more complete model investigationcompared to using the more traditional single best-estimate simulation only.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 7
    Publication Date: 2017-11-02
    Description: Berthierine and chamosite are iron-rich clay minerals that share similar chemical compositions. Berthierine forms at low temperature (25–45 °C) during early diagenesis and may transfer to chamosite at temperatures of ≥70 °C. Because the formation of berthierine and chamosite requires significant amount of Fe 2+ supply, their presence in marine sediments is often used as a mineral proxy for ferruginous conditions in porewater. Recent studies reveal that the Precambrian oceans were characterized by pervasive ferruginous water-column conditions that may favor the formation of iron-rich clay minerals like berthierine and chamosite. To evaluate if ferruginous water-column conditions in the Precambrian ocean played a role on iron-rich clay mineral formation, we conducted an integrated petrographic, mineralogical, and geochemical study on the chamosite- and glauconite-bearing strata of the Mesoproterozoic Xiamaling Formation (~1.40–1.35 Ga) in North China. Petrographic, XRD, SEM, and EDS analyses show that the chamosites of the Xiamaling Formation was transferred from glauconite, with berthierine as an intermediate mineral phase during early diagenesis. Geochemical analyses indicate that a complete transformation from glauconite-dominated to chamosite-dominated end-members (samples) requires an addition of a large amount of Fe (16.9 wt%), Mg (2.4 wt%), and a small amount of Al (1.4 wt%), but a simultaneous release of Si (11.8 wt%) and K (6.0 wt%). Considering that the glauconite- and chamosite-bearing strata are devoid of iron-rich detrital minerals (e.g., biotite and iron oxides) and lack evidence of hydrothermal alteration, the required Fe 2+ for glauconite-berthierine-chamosite transformation was most likely from Fe 2+ -rich (ferruginous) seawater, which may have promoted glauconite-berthierine transformation at the very early diagenetic stage when Fe 2+ exchange between porewater and seawater was still available. This interpretation is consistent with the high Fe HR /Fe T (but low Fe py /Fe HR ), Fe/Al, and V/Al ratios from the hosting strata that support ferruginous depositional environments. Because most Precambrian strata have passed the oil window temperature (〉50–150 °C), the preservation of berthierine would be rare and chamosite should be the representative iron-rich clay mineral. Thus, the abundance of chamosite in fine-grained, marine siliciclastic sediments may be used as a mineral indicator of ferruginous water-column conditions.
    Print ISSN: 0003-004X
    Electronic ISSN: 1945-3027
    Topics: Geosciences
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  • 8
    Publication Date: 2016-05-28
    Description: Ice nucleation is a critical process for the ice crystal formation in cirrus clouds. The relative contribution of homogeneous nucleation versus heterogeneous nucleation to cirrus formation differs between measurements and predictions from general circulation models (GCMs). Here we perform large-ensemble simulations of the ice nucleation process using a cloud parcel model driven by observed vertical motions, and find that homogeneous nucleation occurs rather infrequently, in agreement with recent measurement findings. When the effect of observed vertical velocity fluctuations on ice nucleation is considered in the Community Atmosphere Model version 5 (CAM5), the relative contribution of homogeneous nucleation to cirrus cloud occurrences decreases to only a few percent. However, homogeneous nucleation still has strong impacts on the cloud radiative forcing. Hence, the importance of homogeneous nucleation for cirrus cloud formation should not be dismissed on the global scale.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 9
    Publication Date: 2015-08-25
    Description: Author(s): N. Xu, C. E. Matt, P. Richard, A. van Roekeghem, S. Biermann, X. Shi, S.-F. Wu, H. W. Liu, D. Chen, T. Qian, N. C. Plumb, M. Radović, Hangdong Wang, Qianhui Mao, Jianhua Du, Minghu Fang, J. Mesot, H. Ding, and M. Shi Combining photoemission spectroscopy, Raman spectroscopy, and first-principles calculations, we characterize superconducting TlNi 2 Se 2 as a material with weak electronic Coulomb correlations leading to a bandwidth renormalization of 1.4. We identify a camelback-shaped band, whose energetic position s… [Phys. Rev. B 92, 081116(R)] Published Mon Aug 24, 2015
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 10
    Publication Date: 2016-07-30
    Description: CaFeAs 2 is a parent compound of recently discovered 112-type iron-based superconductors. It is predicted to be a staggered intercalation compound that naturally integrates both quantum spin Hall insulating and superconducting layers and an ideal system for the realization of Majorana modes. We performed a systematical angle-resolved photoemission spectroscopy and first-principles calculation study of the slightly electron-doped CaFeAs 2 . We found that the zigzag As chain of 112-type iron-based superconductors play a considerable role in the low-energy electronic structure, resulting in the characteristic Dirac-cone like band dispersion as the prediction. Our experimental results further confirm that these Dirac cones only exist around the X but not Y points in the Brillouin zone, breaking the S 4 symmetry at iron sites. Our findings present the compelling support to the theoretical prediction that the 112-type iron-based superconductors might host the topological nontrivial edge states. The slightly electron doped CaFeAs 2 would provide us a unique opportunity to realize and explore Majorana fermion physics.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
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