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
  • 1
    facet.materialart.
    Unknown
    Registration of ‘Florico’ Stargrass (1993)
    Wiley
    Details
    Publication Date: 1993-01-01
    Print ISSN: 0011-183X
    Electronic ISSN: 1435-0653
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Wiley
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 2
    facet.materialart.
    Unknown
    Digital development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: Developmental systems biology is poised to exploit large-scale data from two approaches: genomics and live imaging. The combination of the two offers the opportunity to map gene functions and gene networks in vivo at single-cell resolution using cell tracking and quantification of cellular phenotypes. Here we present Digital Development ( http://www.digital-development.org ), a database of cell lineage differentiation with curated phenotypes, cell-specific gene functions and a multiscale model. The database stores data from recent systematic studies of cell lineage differentiation in the C. elegans embryo containing ~200 conserved genes, 1400 perturbed cell lineages and 600 000 digitized single cells. Users can conveniently browse, search and download four categories of phenotypic and functional information from an intuitive web interface. This information includes lineage differentiation phenotypes, cell-specific gene functions, differentiation landscapes and fate choices, and a multiscale model of lineage differentiation. Digital Development provides a comprehensive, curated, multidimensional database for developmental biology. The scale, resolution and richness of biological information presented here facilitate exploration of gene-specific and systems-level mechanisms of lineage differentiation in Metazoans.
    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
  • 3
    facet.materialart.
    Unknown
    Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde (2012)
    Oxford University Press
    Details
    Publication Date: 2012-09-13
    Description: Formaldehyde has long been recognized as a hazardous environmental agent highly reactive with DNA. Recently, it has been realized that due to the activity of histone demethylation enzymes within the cell nucleus, formaldehyde is produced endogenously, in direct vicinity of genomic DNA. Should it lead to extensive DNA damage? We address this question with the aid of a computational mapping method, analogous to X-ray and nuclear magnetic resonance techniques for observing weakly specific interactions of small organic compounds with a macromolecule in order to establish important functional sites. We concentrate on the leading reaction of formaldehyde with free bases: hydroxymethylation of cytosine amino groups. Our results show that in B-DNA, cytosine amino groups are totally inaccessible for the formaldehyde attack. Then, we explore the effect of recently discovered transient flipping of Watson–Crick (WC) pairs into Hoogsteen (HG) pairs (HG breathing). Our results show that the HG base pair formation dramatically affects the accessibility for formaldehyde of cytosine amino nitrogens within WC base pairs adjacent to HG base pairs. The extensive literature on DNA interaction with formaldehyde is analyzed in light of the new findings. The obtained data emphasize the significance of DNA HG breathing.
    Keywords: Nucleic acid structure, Phsyical and Biochemical Characterisation of DNA
    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
  • 4
    facet.materialart.
    Unknown
    Constraining Groundwater Flow in the Glacial Drift and Saginaw Aquifers in the Michigan Basin through Helium Concentrations and Isotopic Ratios (2015)
    Wiley
    In: Geofluids
    Details
    Publication Date: 2015-02-26
    Description: 3 He and 4 He concentrations in excess of those in water in solubility equilibrium with the atmosphere by up to two and three orders of magnitude are observed in the shallow Glacial Drift and Saginaw aquifers in the Michigan Basin. A simplified He transport model shows that in-situ production is negligible and that most He excesses have a source external to the aquifer. Simulated results show that 3 He and 4 He fluxes entering the bottom of the Saginaw aquifer are 7.5×10 -14 and 6.1×10 -7 cm 3 STPcm −2 yr −1 , both of which are lower than fluxes entering the underlying Marshall aquifer, 1.0×10 -13 and 1.6×10 -6 cm 3 STPcm −2 yr −1 for 3 He and 4 He, respectively. In contrast, He fluxes entering the Saginaw aquifer are higher than fluxes entering the overlying Glacial Drift aquifer of 5.2×10 -14 and 1.5 × 10 -7 cm 3 STPcm −2 yr −1 for 3 He and 4 He, respectively. The unusually high He fluxes and their decreasing values from the lower Marshall to the upper Glacial Drift aquifer strongly suggest the presence of an upward cross-formational flow, with increasing He dilution toward the surface by recharge water. These fluxes are either comparable to or far greater than He fluxes in deeper aquifers around the world. Model simulations also suggest an exponential decrease of the horizontal groundwater velocity with recharge distance. Horizontal velocities vary from 13 to 2 myr −1 for the Saginaw aquifer and from 18 to 6 myr −1 for the Marshall aquifer. The highly permeable Glacial Drift aquifer displays a greater velocity range, from 250 to 5 myr −1 . While Saginaw 4 He ages estimated based on the simulated velocity field display an overall agreement with 14 C ages, 14 C and 4 He ages in the Glacial Drift and Marshall aquifers deviate significantly, possibly due to simplifications introduced in the He transport model leading to calculation of first order approximation He ages and high uncertainties in Glacial Drift 14 C ages. This article is protected by copyright. All rights reserved.
    Print ISSN: 1468-8115
    Electronic ISSN: 1468-8123
    Topics: Geosciences
    Published by Wiley
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 5
    facet.materialart.
    Unknown
    Genome-wide association study identifies loci on 12q24 and 13q32 associated with Tetralogy of Fallot (2013)
    Oxford University Press
    Details
    Publication Date: 2013-03-15
    Description: We conducted a genome-wide association study to search for risk alleles associated with Tetralogy of Fallot (TOF), using a northern European discovery set of 835 cases and 5159 controls. A region on chromosome 12q24 was associated ( P = 1.4 x 10 –7 ) and replicated convincingly ( P = 3.9 x 10 –5 ) in 798 cases and 2931 controls [per allele odds ratio (OR) = 1.27 in replication cohort, P = 7.7 x 10 –11 in combined populations]. Single nucleotide polymorphisms in the glypican 5 gene on chromosome 13q32 were also associated ( P = 1.7 x 10 –7 ) and replicated convincingly ( P = 1.2 x 10 –5 ) in 789 cases and 2927 controls (per allele OR = 1.31 in replication cohort, P = 3.03 x 10 –11 in combined populations). Four additional regions on chromosomes 10, 15 and 16 showed suggestive association accompanied by nominal replication. This study, the first genome-wide association study of a congenital heart malformation phenotype, provides evidence that common genetic variation influences the risk of TOF.
    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
  • 6
    facet.materialart.
    Unknown
    FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-25
    Description: Computational solvent mapping finds binding hot spots, determines their druggability and provides information for drug design. While mapping of a ligand-bound structure yields more accurate results, usually the apo structure serves as the starting point in design. The FTFlex algorithm, implemented as a server, can modify an apo structure to yield mapping results that are similar to those of the respective bound structure. Thus, FTFlex is an extension of our FTMap server, which only considers rigid structures. FTFlex identifies flexible residues within the binding site and determines alternative conformations using a rotamer library. In cases where the mapping results of the apo structure were in poor agreement with those of the bound structure, FTFlex was able to yield a modified apo structure, which lead to improved FTMap results. In cases where the mapping results of the apo and bound structures were in good agreement, no new structure was predicted. Availability: FTFlex is freely available as a web-based server at http://ftflex.bu.edu/ . Contact: vajda@bu.edu or midas@bu.edu Supplementary information: Supplementary data 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
  • 7
    facet.materialart.
    Unknown
    Ohno's "Peril of Hemizygosity" Revisited: Gene Loss, Dosage Compensation, and Mutation (2013)
    Oxford University Press
    Details
    Publication Date: 2013-01-06
    Description: We explore the evolutionary origins of dosage compensation (DC) in sex chromosomes in the context of metabolic control theory. We consider first the cost of gene loss (hemizygosity) per se in reducing flux, and examine two relationships between flux and fitness (linear and Gaussian) to calculate a fitness cost of hemizygosity. Recognizing that new sex chromosomes are derived from autosomes, we also calculate the cost of unmasking deleterious mutations segregating on the nascent sex chromosomes as loci become hemizygous. The importance of deleterious mutations to the fitness cost of hemizygosity depends on their frequency, and on the relative costs of halving gene dose for wild-type alleles. We then consider the evolution of DC in response to gene loss, and include a cost of overexpression (i.e., DC such that expression exceeds the wild-type homozygote). Even with costs to excess flux, hypomorphic mutations can cause the optimal level of DC to be higher than 2-fold when the absolute cost of hemizygosity is small. Finally, we propose a three-step model of DC evolution: 1) once recombination ceases and the Y begins to deteriorate, genes from longer metabolic pathways should be lost first, as halving these genes does not drastically reduce flux or, thereby, fitness; 2) both the cost of hemizygosity and the presence of hypomorphic mutations will drive an increase in expression, that is, DC; 3) existing DC will now permit loss of genes in short pathways.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 8
    facet.materialart.
    Unknown
    Application of asymmetric statistical potentials to antibody-protein docking (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-11
    Description: Motivation: An effective docking algorithm for antibody–protein antigen complex prediction is an important first step toward design of biologics and vaccines. We have recently developed a new class of knowledge-based interaction potentials called Decoys as the Reference State (DARS) and incorporated DARS into the docking program PIPER based on the fast Fourier transform correlation approach. Although PIPER was the best performer in the latest rounds of the CAPRI protein docking experiment, it is much less accurate for docking antibody–protein antigen pairs than other types of complexes, in spite of incorporating sequence-based information on the location of the paratope. Analysis of antibody–protein antigen complexes has revealed an inherent asymmetry within these interfaces. Specifically, phenylalanine, tryptophan and tyrosine residues highly populate the paratope of the antibody but not the epitope of the antigen. Results: Since this asymmetry cannot be adequately modeled using a symmetric pairwise potential, we have removed the usual assumption of symmetry. Interaction statistics were extracted from antibody–protein complexes under the assumption that a particular atom on the antibody is different from the same atom on the antigen protein. The use of the new potential significantly improves the performance of docking for antibody–protein antigen complexes, even without any sequence information on the location of the paratope. We note that the asymmetric potential captures the effects of the multi-body interactions inherent to the complex environment in the antibody–protein antigen interface. Availability: The method is implemented in the ClusPro protein docking server, available at http://cluspro.bu.edu . Contact: midas@bu.edu or vajda@bu.edu Supplementary information: Supplementary data 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
  • 9
    facet.materialart.
    Unknown
    An improved model of charge transfer inefficiency and correction algorithm for the Hubble Space Telescope (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-01
    Description: Charge-coupled device (CCD) detectors, widely used to obtain digital imaging, can be damaged by high energy radiation. Degraded images appear blurred, because of an effect known as Charge Transfer Inefficiency (CTI), which trails bright objects as the image is read out. It is often possible to correct most of the trailing during post-processing, by moving flux back to where it belongs. We compare several popular algorithms for this: quantifying the effect of their physical assumptions and tradeoffs between speed and accuracy. We combine their best elements to construct a more accurate model of damaged CCDs in the Hubble Space Telescope 's Advanced Camera for Surveys / Wide Field Channel , and update it using data up to early 2013. Our algorithm now corrects 98 per cent of CTI trailing in science exposures, a substantial improvement over previous work. Further progress will be fundamentally limited by the presence of read noise. Read noise is added after charge transfer so does not get trailed – but it is incorrectly untrailed during post-processing.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 10
    facet.materialart.
    Unknown
    Peak Tremor Rates Lead Peak Slip Rates During Propagation of Two Large Slow Earthquakes in Cascadia (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: Abstract We explore the evolution of slow slip on the Cascadia megathrust during two large episodic tremor and slip (ETS) events and compare stress changes to the spatial evolution of tremor from PNSN tremor locations. We used displacement time series from ~72 GPS stations, along with the Extended Network Inversion Filter to solve for the time‐dependent fault slip. The 2010 (Mw 6.8) and 2012 (Mw 6.8) events propagated northward and southward, respectively, allowing us to assess directional effects on slip behavior. We observed that tremor occurs on the leading edge of propagating slipping regions, well ahead of the highest slip rates, independent of the along‐strike propagation direction. Resolution tests using the actual tremor distributions to generate synthetic data show that our result of peak tremor rates leading peak slip rates is not due to biases introduced by temporal smoothing. Calculated stress changes due to the time‐dependent slip distributions imply that tremor is sensitive to kPa's of stress, consistent with studies of tidally‐triggered tremor. Within the resolution of our model, our results are consistent with the hypothesis that significant tremor is triggered by stresses ahead of the highest slip rates. We also observe ongoing slip continuing several days after tremor has passed. Our observations are consistent with some numerical models of tremor patches that suggest that this behavior can be explained by densely packed asperities resulting in somewhat crack‐like propagation rather than a slip pulse that is as concentrated as the tremor activity.
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
    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...