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  • 1
    Publication Date: 2016-07-29
    Description: 1RXS J180408.9–342058 is a transient neutron star low-mass X-ray binary that exhibited a bright accretion outburst in 2015. We present NuSTAR , Swift , and Chandra observations obtained around the peak brightness of this outburst. The source was in a soft X-ray spectral state and displayed an X-ray luminosity of L X ~= (2–3)  x  10 37 ( D /5.8 kpc) 2 erg s –1 (0.5–10 keV). The NuSTAR data reveal a broad Fe–K emission line that we model as relativistically broadened reflection to constrain the accretion geometry. We found that the accretion disc is viewed at an inclination of i ~= 27°–35° and extended close to the neutron star, down to R in ~= 5–7.5 gravitational radii (~=11–17 km). This inner disc radius suggests that the neutron star magnetic field strength is B 2  x  10 8  G. We find a narrow absorption line in the Chandra /HEG data at an energy of ~=7.64 keV with a significance of ~=4.8. This feature could correspond to blueshifted Fe  xxvi and arise from an accretion disc wind, which would imply an outflow velocity of v out ~= 0.086 c (~=25 800 km s –1 ). However, this would be extreme for an X-ray binary and it is unclear if a disc wind should be visible at the low inclination angle that we infer from our reflection analysis. Finally, we discuss how the X-ray and optical properties of 1RXS J180408.9–342058 are consistent with a relatively small ( P orb 3 h) binary orbit.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 2
    Publication Date: 2016-06-21
    Description: Mitochondrial DNA (mtDNA) rearrangements are an important cause of mitochondrial disease and age related mitochondrial dysfunction in tissues including brain and skeletal muscle. It is known that different mtDNA deletions accumulate in single cells, but the detailed nature of these rearrangements is still unknown. To evaluate this we used a complementary set of sensitive assays to explore the mtDNA rearrangements in individual cells from patients with sporadic inclusion body myositis, a late-onset inflammatory myopathy with prominent mitochondrial changes. We identified large-scale mtDNA deletions in individual muscle fibres with 20% of cytochrome c oxidase-deficient myofibres accumulating two or more mtDNA deletions. The majority of deletions removed only the major arc but ~10% of all deletions extended into the minor arc removing the origin of light strand replication (O L ) and a variable number of genes. Some mtDNA molecules contained two deletion sites. Additionally, we found evidence of mitochondrial genome duplications allowing replication and clonal expansion of these complex rearranged molecules. The extended spectrum of mtDNA rearrangements in single cells provides insight into the process of clonal expansion which is fundamental to our understanding of the role of mtDNA mutations in ageing and disease.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2013-06-07
    Description: Neuronal ceroid lipofuscinosis (NCL), commonly referred to as Batten disease, is a group of autosomal recessive neurodegenerative diseases of childhood characterized by seizures, blindness, motor and cognitive decline and premature death. Currently, there are over 400 known mutations in 14 different genes, leading to five overlapping clinical variants of NCL. A large portion of these mutations lead to premature stop codons (PTCs) and are predicted to predispose mRNA transcripts to nonsense-mediated decay (NMD). Nonsense-mediated decay is associated with a number of other genetic diseases and is an important regulator of disease pathogenesis. We contend that NMD targets PTCs in NCL gene transcripts for degradation. A number of PTC mutations in CLN1 , CLN2 and CLN3 lead to a significant decrease in mRNA transcripts and a corresponding decrease in protein levels and function in patient-derived lymphoblast cell lines. Inhibiting NMD leads to an increased transcript level, and where protein function is known, increased activity. Treatment with read-through drugs also leads to increased protein function. Thus, NMD provides a promising therapeutic target that would allow read-through of transcripts to enhance protein function and possibly ameliorate Batten disease pathogenesis.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 4
    Publication Date: 2013-04-03
    Description: Bent-double radio sources have been used as a probe to measure the density of intergalactic gas in galaxy groups. We carry out a series of high-resolution, three-dimensional simulations of active galactic nucleus (AGN) jets moving through an external medium with a constant density in order to develop a general formula for the radius of curvature of the jets, and to determine how accurately the density of the intra-group medium (IGM) can be measured. Our simulations produce curved jets ending in bright radio lobes with an extended trail of low surface brightness radio emission. The radius of curvature of the jets varies with time by only about 25 per cent. The radio trail seen in our simulations is typically not detected in known sources, but may be detectable in lower resolution radio observations. The length of this tail can be used to determine the age of the AGN. We also use our simulation data to derive a formula for the kinetic luminosity of observed jets in terms of the radius of curvature and jet pressure. In characterizing how well observations can measure the IGM density, we find that the limited resolution of typical radio observations leads to a systematic underestimate of the IGM density of about 50 per cent. The unknown angles between the observer and the direction of jet propagation and direction of AGN motion through the IGM lead to an uncertainty of about ±50 per cent in estimates of the IGM density. Previous conclusions drawn using these sources, indicating that galaxy groups contain significant reservoirs of baryons in their IGM, are still valid when considering this level of uncertainty. In addition, we model the X-ray emission expected from bent-double radio sources. We find that known sources in reasonably dense environments should be detectable in ~100 ks Chandra observations. X-ray observations of these sources would place constraints on the IGM density and AGN velocity that are complementary to radio observations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 5
    Publication Date: 2015-04-07
    Print ISSN: 0302-3427
    Electronic ISSN: 1471-5430
    Topics: Nature of Science, Research, Systems of Higher Education, Museum Science
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  • 6
    Publication Date: 2015-07-07
    Description: Developmental changes in the temporal and spatial regulation of gene expression drive the emergence of normal mature brain function, while disruptions in these processes underlie many neurodevelopmental abnormalities. To solidify our foundational knowledge of such changes in a primate brain with an extended period of postnatal maturation like in human, we investigated the whole-genome transcriptional profiles of rhesus monkey brains from birth to adulthood. We found that gene expression dynamics are largest from birth through infancy, after which gene expression profiles transition to a relatively stable state by young adulthood. Biological pathway enrichment analysis revealed that genes more highly expressed at birth are associated with cell adhesion and neuron differentiation, while genes more highly expressed in juveniles and adults are associated with cell death. Neocortex showed significantly greater differential expression over time than subcortical structures, and this trend likely reflects the protracted postnatal development of the cortex. Using network analysis, we identified 27 co-expression modules containing genes with highly correlated expression patterns that are associated with specific brain regions, ages or both. In particular, one module with high expression in neonatal cortex and striatum that decreases during infancy and juvenile development was significantly enriched for autism spectrum disorder (ASD)-related genes. This network was enriched for genes associated with axon guidance and interneuron differentiation, consistent with a disruption in the formation of functional cortical circuitry in ASD.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 7
    Publication Date: 2012-09-28
    Description: Facioscapulohumeral muscular dystrophy (FSHD), the most prevalent myopathy afflicting both children and adults, is predominantly associated with contractions in the 4q35-localized macrosatellite D4Z4 repeat array. Recent studies have proposed that FSHD pathology is caused by the misexpression of the DUX4 (double homeobox 4) gene resulting in production of a pathogenic protein, DUX4-FL, which has been detected in FSHD, but not in unaffected control myogenic cells and muscle tissue. Here, we report the analysis of DUX4 mRNA and protein expression in a much larger collection of myogenic cells and muscle biopsies derived from biceps and deltoid muscles of FSHD affected subjects and their unaffected first-degree relatives. We confirmed that stable DUX4-fl mRNA and protein were expressed in myogenic cells and muscle tissues derived from FSHD affected subjects, including several genetically diagnosed adult FSHD subjects yet to show clinical manifestations of the disease in the assayed muscles. In addition, we report DUX4-fl mRNA and protein expression in muscle biopsies and myogenic cells from genetically unaffected relatives of the FSHD subjects, although at a significantly lower frequency. These results establish that DUX4-fl expression per se is not sufficient for FSHD muscle pathology and indicate that quantitative modifiers of DUX4-fl expression and/or function and family genetic background are determinants of FSHD muscle disease progression.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 8
    Publication Date: 2016-01-16
    Description: Observational evidence has been accumulating that thermonuclear X-ray bursts ignited on the surface of neutron stars influence the surrounding accretion flow. Here, we exploit the excellent sensitivity of NuSTAR up to 79 keV to analyse the impact of an X-ray burst on the accretion emission of the neutron star LMXB 4U 1608–52. The ~=200 s long X-ray burst occurred during a hard X-ray spectral state, and had a peak intensity of ~=30–50 per cent of the Eddington limit with no signs of photospheric radius expansion. Spectral analysis suggests that the accretion emission was enhanced up to a factor of ~=5 during the X-ray burst. We also applied a linear unsupervised decomposition method, namely non-negative matrix factorization (NMF), to study this X-ray burst. We find that the NMF performs well in characterizing the evolution of the burst emission and is a promising technique to study changes in the underlying accretion emission in more detail than is possible through conventional spectral fitting. For the burst of 4U 1608–52, the NMF suggests a possible softening of the accretion spectrum during the X-ray burst, which could potentially be ascribed to cooling of a corona. Finally, we report a small (~=3 per cent) but significant rise in the accretion emission ~=0.5 h before the X-ray burst, although it is unclear whether this was related to the X-ray burst ignition.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 9
    Publication Date: 2012-06-24
    Description: Motivation: Liquid chromatography–mass spectrometry-based metabolomics has gained importance in the life sciences, yet it is not supported by software tools for high throughput identification of metabolites based on their fragmentation spectra. An algorithm (ISIS: in silico identification software) and its implementation are presented and show great promise in generating in silico spectra of lipids for the purpose of structural identification. Instead of using chemical reaction rate equations or rules-based fragmentation libraries, the algorithm uses machine learning to find accurate bond cleavage rates in a mass spectrometer employing collision-induced dissociation tandem mass spectrometry. Results: A preliminary test of the algorithm with 45 lipids from a subset of lipid classes shows both high sensitivity and specificity. Contact: lars.kangas@pnnl.gov 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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  • 10
    Publication Date: 2011-11-24
    Description: We prove that every sufficiently slow-growing diagonally non-recursive (DNR) function computes a real with effective Hausdorff dimension 1. We then show that, for any recursive unbounded and non-decreasing function j , there is a DNR function bounded by j that does not compute a Martin-Löf random real. Hence, there is a real of effective Hausdorff dimension 1 that does not compute a Martin-Löf random real. This answers a question of Reimann and Terwijn.
    Print ISSN: 0024-6093
    Electronic ISSN: 1469-2120
    Topics: Mathematics
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