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  • 1
    Publication Date: 2015-06-05
    Description: In the low-redshift Universe, the most powerful radio sources are often associated with gas-rich galaxy mergers or interactions. We here present evidence for an advanced, gas-rich (‘wet’) merger associated with a powerful radio galaxy at a redshift of z  ~ 2. This radio galaxy, MRC 0152-209, is the most infrared-luminous high-redshift radio galaxy known in the Southern hemisphere. Using the Australia Telescope Compact Array, we obtained high-resolution CO(1–0) data of cold molecular gas, which we complement with Hubble Space Telescope ( HST )/ Wide Field Planetary Camera 2 ( WFPC 2) imaging and William Herschel Telescope long-slit spectroscopy. We find that, while roughly M H2  ~ 2 10 10  M of molecular gas coincides with the central host galaxy, another M H2  ~ 3 10 10  M is spread across a total extent of ~60 kpc. Most of this widespread CO(1–0) appears to follow prominent tidal features visible in the rest-frame near-UV HST / WFPC 2 imaging. Lyα emission shows an excess over He II, but a deficiency over L IR , which is likely the result of photoionization by enhanced but very obscured star formation that was triggered by the merger. In terms of feedback, the radio source is aligned with widespread CO(1–0) emission, which suggests that there is a physical link between the propagating radio jets and the presence of cold molecular gas on scales of the galaxy's halo. Its optical appearance, combined with the transformational stage at which we witness the evolution of MRC 0152-209, leads us to adopt the name ‘Dragonfly Galaxy’.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 2
    Publication Date: 2016-07-30
    Description: Motivation: Similarity-based methods have been widely used in order to infer the properties of genes and gene products containing little or no experimental annotation. New approaches that overcome the limitations of methods that rely solely upon sequence similarity are attracting increased attention. One of these novel approaches is to use the organization of the structural domains in proteins. Results: We propose a method for the automatic annotation of protein sequences in the UniProt Knowledgebase (UniProtKB) by comparing their domain architectures, classifying proteins based on the similarities and propagating functional annotation. The performance of this method was measured through a cross-validation analysis using the Gene Ontology (GO) annotation of a sub-set of UniProtKB/Swiss-Prot. The results demonstrate the effectiveness of this approach in detecting functional similarity with an average F-score: 0.85. We applied the method on nearly 55.3 million uncharacterized proteins in UniProtKB/TrEMBL resulted in 44 818 178 GO term predictions for 12 172 114 proteins. 22% of these predictions were for 2 812 016 previously non-annotated protein entries indicating the significance of the value added by this approach. Availability and implementation: The results of the method are available at: ftp://ftp.ebi.ac.uk/pub/contrib/martin/DAAC/ . Contact: tdogan@ebi.ac.uk 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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  • 3
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    Oxford University Press
    Publication Date: 2016-06-16
    Description: Motivation: Read-based phasing deduces the haplotypes of an individual from sequencing reads that cover multiple variants, while genetic phasing takes only genotypes as input and applies the rules of Mendelian inheritance to infer haplotypes within a pedigree of individuals. Combining both into an approach that uses these two independent sources of information—reads and pedigree—has the potential to deliver results better than each individually. Results: We provide a theoretical framework combining read-based phasing with genetic haplotyping, and describe a fixed-parameter algorithm and its implementation for finding an optimal solution. We show that leveraging reads of related individuals jointly in this way yields more phased variants and at a higher accuracy than when phased separately, both in simulated and real data. Coverages as low as 2 x for each member of a trio yield haplotypes that are as accurate as when analyzed separately at 15 x coverage per individual. Availability and Implementation: https://bitbucket.org/whatshap/whatshap Contact: t.marschall@mpi-inf.mpg.de
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 4
    Publication Date: 2015-06-23
    Description: The pathological accumulation of abnormally hyperphosphorylated and aggregated tau, a neuronal microtubule (MT)-associated protein that functions to maintain MT stability, is implicated in a number of hereditary and sporadic neurodegenerative diseases including frontotemporal dementia and Alzheimer's disease. Targeting tau for the treatment of these diseases is an area of intense interest and toward that end, modulation of cellular molecular chaperones is a potential therapeutic target. In particular, the constitutive Hsp70 isoform, Hsc70, seems highly interconnected with tau, preserving tau protein levels and synergizing with it to assemble MTs. But the relationship between tau and Hsc70, as well as the impact of this interaction in neurons and its therapeutic implications remain unknown. Using a human dominant negative Hsc70 that resembles isoform selective inhibition of this important chaperone, we found for the first time that Hsc70 activity is required to stimulate MT assembly in cells and brain. However, surprisingly, active Hsc70 also requires active tau to regulate MT assembly in vivo , suggesting that tau acts in some ways as a co-chaperone for Hsc70 to coordinate MT assembly. This was despite tau binding to Hsc70 as substrate, as determined biochemically. Moreover, we show that while chronic Hsc70 inhibition damaged MT dynamics, intermittent treatment with a small molecule Hsp70 inhibitor lowered tau in brain tissue without disrupting MT integrity. Thus, in tauopathies, where MT injury would be detrimental to neurons, the unique relationship of tau with the Hsc70 machinery can be exploited to deplete tau levels without damaging MT networks.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 5
    Publication Date: 2015-01-21
    Description: A significant minority of high-redshift radio galaxy (HzRG) candidates show extremely red broad-band colours and remain undetected in emission lines after optical ‘discovery’ spectroscopy. In this paper, we present deep GTC optical imaging and spectroscopy of one such radio galaxy, 5C 7.245, with the aim of better understanding the nature of these enigmatic objects. Our g -band image shows no significant emission coincident with the stellar emission of the host galaxy, but does reveal faint emission offset by ~3 arcsec (26 kpc) therefrom along a similar position angle to that of the radio jets, reminiscent of the ‘alignment effect’ often seen in the optically luminous HzRGs. This offset g -band source is also detected in several UV emission lines, giving it a redshift of 1.609, with emission line flux ratios inconsistent with photoionization by young stars or an AGN, but consistent with ionization by fast shocks. Based on its unusual gas geometry, we argue that in 5C 7.245 we are witnessing a rare (or rarely observed) phase in the evolution of quasar hosts when stellar mass assembly, accretion on to the back hole, and powerful feedback activity has eradicated its cold gas from the central ~20 kpc, but is still in the process of cleansing cold gas from its extended halo.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 6
    Publication Date: 2015-09-24
    Description: We study the physical and kinematic properties of the narrow-line region (NLR) of the nearest obscured quasar MRK 477 ( z  = 0.037), using optical and near-infrared (NIR) spectroscopy. About 100 emission lines are identified in the optical+NIR spectrum (90 in the optical), including several narrow optical Fe + lines. To our knowledge, this is the first type 2 active galactic nucleus (AGN) with such a detection. The Fe + lines can be explained as the natural emission from the NLR photoionized by the AGN. Coronal line emission can only be confirmed in the NIR spectrum. As in many other AGNs, a significant correlation is found between the lines’ full width at half-maximum and the critical density log( n crit ). We propose that it is caused by the outflow. This could be the case in other AGNs. The nuclear jet-induced ionized outflow has been kinematically isolated in many emission lines covering a broad range of ionization potentials and critical densities. It is concentrated within R ~few x 100 pc from the central engine. The outflowing gas is denser ( n 8000 cm –3 ) than the ambient non-perturbed gas ( n  ~ 400–630 cm –3 ). This could be due to the compression effect of the jet-induced shocks. Alternatively, we propose that the outflow has been triggered by the jet at R 220 pc (possibly at 30 pc), and we trace how the impact weakens as it propagates outwards following the radiation-pressure-dominated density gradient. The different kinematic behaviour of [Fe  ii ] 1.644 μm suggests that its emission is enhanced by shocks induced by the nuclear outflow/jet and is preferentially emitted at a different, less reddened spatial location.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 7
    Publication Date: 2016-01-24
    Description: As the oomycete pathogen causing potato late blight disease, Phytophthora infestans triggered the famous 19th-century Irish potato famine and remains the leading cause of global commercial potato crop destruction. But the geographic origin of the genotype that caused this devastating initial outbreak remains disputed, as does the New World center of origin of the species itself. Both Mexico and South America have been proposed, generating considerable controversy. Here, we readdress the pathogen’s origins using a genomic data set encompassing 71 globally sourced modern and historical samples of P. infestans and the hybrid species P. andina , a close relative known only from the Andean highlands. Previous studies have suggested that the nuclear DNA lineage behind the initial outbreaks in Europe in 1845 is now extinct. Analysis of P. andina ’s phased haplotypes recovered eight haploid genome sequences, four of which represent a previously unknown basal lineage of P. infestans closely related to the famine-era lineage. Our analyses further reveal that clonal lineages of both P. andina and historical P. infestans diverged earlier than modern Mexican lineages, casting doubt on recent claims of a Mexican center of origin. Finally, we use haplotype phasing to demonstrate that basal branches of the clade comprising Mexican samples are occupied by clonal isolates collected from wild Solanum hosts, suggesting that modern Mexican P. infestans diversified on Solanum tuberosum after a host jump from a wild species and that the origins of P. infestans are more complex than was previously thought.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 8
    Publication Date: 2016-01-20
    Description: Ultraviolet (UV) colors are visual signals potentially involved in territorial conflicts. However, the role of UV signals remains unclear relative to the prior resident effect and familiarity with the opponent, and the reliability of UV signals is still controversial. Male common lizards Zootoca vivipara exhibit substantial variation in the reflectance of their throat UV color patch. We tested whether UV reflectance was correlated with indicators of individual condition. We further manipulated throat UV reflectance of resident and intruder lizards and staged repeated encounters in the laboratory during the mating season. We found no evidence of condition dependence of the UV colors expression. During the first encounter among unfamiliar males, a reduction of UV reflectance of 1 of the 2 opponents influenced agonistic behaviors and the contest outcome, such that there was a significant advantage for residents over intruders. This advantage disappeared when both opponents were UV reduced. During the subsequent encounters among familiar males, fighting was more aggressive when opponents displayed similar UV signals, but UV signals did not influence the contest outcome. These results demonstrate that UV reflectance acted as a badge of status in male common lizards whose effects on the behavioral response were modulated, but not overridden, by the prior resident effect and by the familiarity effect. Male–male interactions are therefore mediated by UV signaling and competition for mates should play a major role in the evolutionary maintenance of this ornament. We discuss putative functions and reliability of UV signals.
    Print ISSN: 1045-2249
    Electronic ISSN: 1465-7279
    Topics: Biology
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  • 9
    Publication Date: 2012-04-10
    Description: Peck, M. A., Kanstinger, P., Holste, L., and Martin, M. 2012. Thermal windows supporting survival of the earliest life stages of Baltic herring ( Clupea harengus ). – ICES Journal of Marine Science, 69: 529–536. Projecting climate-driven changes in marine systems will require knowledge on how thermal windows affect the vital rates of key species. To examine the potential, direct effect of climate-driven warming on southwest Baltic herring, we quantified the survival, development, and biochemical condition of embryos (eggs and yolk-sac larvae) at ten temperatures between 2.9 and 21.7°C. Viable hatch was highest from 7 to 13°C, 〈20% at 2.9°C and 0% at 21.7°C. Between 5 and 19°C, increasing temperature ( T ) decreased the time to 50% hatch ( H t , h,): H t = 4461.9 x T – 1.24 ( r 2 = 0.98, p 〈 0.0001). Using degree-days [°d = T (°C) x age (d)] could normalize some (but not all) thermal effects. Most hatching occurred 90–120°d post-fertilization, unfed larvae lost 0.33 µg dry mass ( DM ) °d –1 , larvae did not survive 〉160°d post-hatch. RNA–DNA ratios rapidly decreased between 50 and 80°d post-hatch, whereas DNA x DM –1 increased throughout the yolk-sac phase and likely provides a stronger indicator of irreversible starvation. The critical, "mixed feeding" stage is likely 60–100°d post-hatch. The broad thermal tolerance of herring embryos makes "direct", negative effects of warming unlikely; however, a lack of common methods among studies makes it difficult to project how climate warming will affect embryos of different fish populations and species.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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  • 10
    Publication Date: 2011-11-24
    Description: This paper focuses on the performance evaluation of Compiler for Portable Checkpointing (CPPC), a tool for the checkpointing of parallel message-passing applications. Its performance and the factors that impact it are transparently and rigorously identified and assessed. The tests were performed on a public supercomputing infrastructure, using a large number of very different applications and showing excellent results in terms of performance and effort required for integration into user codes. Statistical analysis techniques have been used to better approximate the performance of the tool. Quantitative and qualitative comparisons with other rollback-recovery approaches to fault tolerance are also included. All these data and comparisons are then discussed in an effort to extract meaningful conclusions about the state-of-the-art and future research trends in the rollback-recovery field.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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