ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
Collection
Keywords
Publisher
Language
Years
  • 1
    facet.materialart.
    Unknown
    Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-03
    Description: Characterization of cell type specific regulatory networks and elements is a major challenge in genomics, and emerging strategies frequently employ high-throughput genome-wide assays of transcription factor (TF) to DNA binding, histone modifications or chromatin state. However, these experiments remain too difficult/expensive for many laboratories to apply comprehensively to their system of interest. Here, we explore the potential of elucidating regulatory systems in varied cell types using computational techniques that rely on only data of gene expression, low-resolution chromatin accessibility, and TF–DNA binding specificities (‘motifs’). We show that static computational motif scans overlaid with chromatin accessibility data reasonably approximate experimentally measured TF–DNA binding. We demonstrate that predicted binding profiles and expression patterns of hundreds of TFs are sufficient to identify major regulators of ~200 spatiotemporal expression domains in the Drosophila embryo. We are then able to learn reliable statistical models of enhancer activity for over 70 expression domains and apply those models to annotate domain specific enhancers genome-wide. Throughout this work, we apply our motif and accessibility based approach to comprehensively characterize the regulatory network of fruitfly embryonic development and show that the accuracy of our computational method compares favorably to approaches that rely on data from many experimental assays.
    Keywords: Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 2
    facet.materialart.
    Unknown
    Experimental study of ^{26}Al through the 1n pick-up reaction ^{27}Al(d,t) (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-05-13
    Description: Author(s): Vishal Srivastava, C. Bhattacharya, T. K. Rana, S. Manna, S. Kundu, S. Bhattacharya, K. Banerjee, P. Roy, R. Pandey, G. Mukherjee, T. K. Ghosh, J. K. Meena, T. Roy, A. Chaudhuri, M. Sinha, A. Saha, Md. A. Asgar, A. Dey, Subinit Roy, and Md. M. Shaikh The Al 27 ( d , t ) reaction has been studied to extract spectroscopic information for the odd-odd nucleus Al 26 . The excited states of Al 26 up to 5.50 MeV have been analyzed using the local, zero range distorted wave Born approximation. A new set of optical model potential parameters was extracted from th... [Phys. Rev. C 91, 054611] Published Mon May 11, 2015
    Keywords: Nuclear Reactions
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
    Published by American Physical Society (APS)
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 3
    facet.materialart.
    Unknown
    Atmospheric 14C/12C changes during the last glacial period from Hulu Cave (2018)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2018
    Description: 〈p〉Paired measurements of 〈sup〉14〈/sup〉C/〈sup〉12〈/sup〉C and 〈sup〉230〈/sup〉Th ages from two Hulu Cave stalagmites complete a precise record of atmospheric 〈sup〉14〈/sup〉C covering the full range of the 〈sup〉14〈/sup〉C dating method (~54,000 years). Over the last glacial period, atmospheric 〈sup〉14〈/sup〉C/〈sup〉12〈/sup〉C ranges from values similar to modern values to values 1.70 times higher (42,000 to 39,000 years ago). The latter correspond to 〈sup〉14〈/sup〉C ages 5200 years less than calibrated ages and correlate with the Laschamp geomagnetic excursion followed by Heinrich Stadial 4. Millennial-scale variations are largely attributable to Earth’s magnetic field changes and in part to climate-related changes in the oceanic carbon cycle. A progressive shift to lower 〈sup〉14〈/sup〉C/〈sup〉12〈/sup〉C values between 25,000 and 11,000 years ago is likely related, in part, to progressively increasing ocean ventilation rates.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 4
    facet.materialart.
    Unknown
    GABA receptor regulation on axon and dendrites [Neuroscience] (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-10-14
    Description: Neuronal output is modulated by inhibition onto both dendrites and axons. It is unknown whether inhibitory synapses at these two cellular compartments of an individual neuron are regulated coordinately or separately during in vivo development. Because neurotransmission influences synapse maturation and circuit development, we determined how loss of inhibition affects...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 5
    facet.materialart.
    Unknown
    Giant nonreciprocal emission of spin waves in Ta/Py bilayers (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-07-03
    Description: Spin waves are propagating disturbances in the magnetization of magnetic materials. One of their interesting properties is nonreciprocity, exhibiting that their amplitude depends on the magnetization direction. Nonreciprocity in spin waves is of great interest in both fundamental science and applications because it offers an extra knob to control the flow of waves for the technological fields of logics and switch applications. We show a high nonreciprocity in spin waves from Ta/Py bilayer systems with out-of-plane magnetic fields. The nonreciprocity depends on the thickness of Ta underlayer, which is found to induce an interfacial anisotropy. The origin of observed high nonreciprocity is twofold: different polarities of the in-plane magnetization due to different angles of canted out-of-plane anisotropy and the spin pumping effect at the Ta/Py interface. Our findings provide an opportunity to engineer highly efficient, nonreciprocal spin wave–based applications, such as nonreciprocal microwave devices, magnonic logic gates, and information transports.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 6
    facet.materialart.
    Unknown
    The role of break-up localization in microcontinent separation along a strike-slip margin: the East India-Elan Bank case study (2015)
    Geological Society (of London)
    Details
    Publication Date: 2015-12-16
    Description: The Elan Bank microcontinent was separated from East India during the Early Cretaceous break-up. The crustal architecture and rifting geometry of East India and the Elan Bank margins document that the early break-up between India and Antarctica was initiated in the eastern portions of the Cauvery and Krishna–Godavari rift zones, and in the southern portion of Elan Bank. However, the westwards break-up propagation along the Krishna–Godavari Rift Zone continued even after the break-up in the overstepping portion of the Cauvery Rift Zone. Eventually, the western propagating end of the Krishna–Godavari Rift Zone became hard-linked with the failed western portion of the Cauvery Rift Zone by the dextral Coromandel transfer fault zone. Consequently, the break-up location between India and Antarctica shifted from its initial to its final location along the northern portion of the Elan Bank formed by the western Krishna–Godavari Rift Zone. The competition between the two rift zones to capture continental break-up and asymmetric ridge propagation resulted in a ridge jump and the Elan Bank microcontinent release. Supplementary material: Supplementary figures are available at http://www.geolsoc.org.uk/SUP18864
    Print ISSN: 0305-8719
    Electronic ISSN: 2041-4927
    Topics: Geosciences
    Published by Geological Society (of London)
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 7
    facet.materialart.
    Unknown
    Primed cytotoxic cells eliminate chimeric partners [Immunology and Inflammation] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-06-08
    Description: In a primitive chordate model of natural chimerism, one chimeric partner is often eliminated in a process of allogeneic resorption. Here, we identify the cellular framework underlying loss of tolerance to one partner within a natural Botryllus schlosseri chimera. We show that the principal cell type mediating chimeric partner elimination...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 8
    facet.materialart.
    Unknown
    Enhanced J-protein interaction and compromised protein stability of mtHsp70 variants lead to mitochondrial dysfunction in Parkinson's disease (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-10
    Description: Parkinson's disease (PD) is the second most prevalent progressive neurological disorder commonly associated with impaired mitochondrial function in dopaminergic neurons. Although familial PD is multifactorial in nature, a recent genetic screen involving PD patients identified two mitochondrial Hsp70 variants (P509S and R126W) that are suggested in PD pathogenesis. However, molecular mechanisms underlying how mtHsp70 PD variants are centrally involved in PD progression is totally elusive. In this article, we provide mechanistic insights into the mitochondrial dysfunction associated with human mtHsp70 PD variants. Biochemically, the R126W variant showed severely compromised protein stability and was found highly susceptible to aggregation at physiological conditions. Strikingly, on the other hand, the P509S variant exhibits significantly enhanced interaction with J-protein cochaperones involved in folding and import machinery, thus altering the overall regulation of chaperone-mediated folding cycle and protein homeostasis. To assess the impact of mtHsp70 PD mutations at the cellular level, we developed yeast as a model system by making analogous mutations in Ssc1 ortholog. Interestingly, PD mutations in yeast (R103W and P486S) exhibit multiple in vivo phenotypes, which are associated with ‘mitochondrial dysfunction’, including compromised growth, impairment in protein translocation, reduced functional mitochondrial mass, mitochondrial DNA loss, respiratory incompetency and increased susceptibility to oxidative stress. In addition to that, R103W protein is prone to aggregate in vivo due to reduced stability, whereas P486S showed enhanced interaction with J-proteins, thus remarkably recapitulating the cellular defects that are observed in human PD variants. Taken together, our findings provide evidence in favor of direct involvement of mtHsp70 as a susceptibility factor in PD.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 9
    facet.materialart.
    Unknown
    Imaging prior information in the brain [Psychological and Cognitive Sciences] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-05-16
    Description: In making sense of the visual world, the brain's processing is driven by two factors: the physical information provided by the eyes (“bottom-up” data) and the expectancies driven by past experience (“top-down” influences). We use degraded stimuli to tease apart the effects of bottom-up and top-down processes because they are easier to recognize with prior knowledge of undegraded images. Using machine learning algorithms, we quantify the amount of information that brain regions contain about stimuli as the subject learns the coherent images. Our results show that several distinct regions, including high-level visual areas and the retinotopic cortex, contain more information about degraded stimuli with prior knowledge. Critically, these regions are separate from those that exhibit classical priming, indicating that top-down influences are more than feature-based attention. Together, our results show how the neural processing of complex imagery is rapidly influenced by fleeting experiences.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 10
    facet.materialart.
    Unknown
    Testing multiple biological mediators simultaneously (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-16
    Description: Motivation:  Modern biomedical and epidemiological studies often measure hundreds or thousands of biomarkers, such as gene expression or metabolite levels. Although there is an extensive statistical literature on adjusting for ‘multiple comparisons’ when testing whether these biomarkers are directly associated with a disease, testing whether they are biological mediators between a known risk factor and a disease requires a more complex null hypothesis, thus offering additional methodological challenges. Results:  We propose a permutation approach that tests multiple putative mediators and controls the family wise error rate. We demonstrate that, unlike when testing direct associations, replacing the Bonferroni correction with a permutation approach that focuses on the maximum of the test statistics can significantly improve the power to detect mediators even when all biomarkers are independent. Through simulations, we show the power of our method is 2–5 x larger than the power achieved by Bonferroni correction. Finally, we apply our permutation test to a case-control study of dietary risk factors and colorectal adenoma to show that, of 149 test metabolites, docosahexaenoate is a possible mediator between fish consumption and decreased colorectal adenoma risk. Availability and implementation:  R-package included in online Supplementary Material. Contact:   joshua.sampson@nih.gov Supplementary information:   Supplementary materials are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...