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  • 1
    Publication Date: 2015-10-03
    Description: We infer the emission positions of twin kilohertz quasi-periodic oscillations (kHz QPOs) in neutron star low-mass X-ray binaries (NS-LMXBs) based on the Alfvén wave oscillation model (AWOM). For most sources, the emission radii of kHz QPOs cluster around a region of 16–19 km with the assumed NS radii of 15 km. Cir X-1 has the larger emission radii of 23 ~ 38 km than those of the other sources, which may be ascribed to its large magnetosphere-disc radius or strong NS surface magnetic field. SAX J1808.4–3658 is also a particular source with the relative large emission radii of kHz QPOs of 20 ~ 23 km, which may be due to its large inferred NS radius of 18 ~ 19 km. The emission radii of kHz QPOs for all the sources are larger than the NS radii, and the possible explanations of which are presented. The similarity of the emission radii of kHz QPOs (~16–19 km) for both the low/high luminosity Atoll/Z sources is found, which indicates that both sources share the similar magnetosphere-disc radii.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 2
    Publication Date: 2013-10-12
    Description: We test the relativistic precession model (RPM) and the magnetohydrodynamics Alfvén wave oscillation model (AWOM) for the kilohertz (kHz) quasi-periodic oscillations (QPOs) from sources with measured neutron star (NS) masses and twin kHz QPO frequencies. For the RPM, the derived NS masses of Cyg X-2, SAX J1808.4–3658 and 4U 1820–30 are 1.96 ± 0.10, 2.83 ± 0.04 and 1.85 ± 0.02 M , respectively. These are, respectively, ~30, 100 and 40 per cent higher than the measured results 1.5 ± 0.3, 〈1.4 and $1.29^{+0.19}_{-0.07}$ M . For the AWOM, where the free parameter of the model is the density of the star, we infer the NS radii to be around 10–20 km for the above three sources. Based on this, we can infer the matter compositions inside the NSs with the help of the equations of state. In particular, for SAX J1808.4–3658, the AWOM shows a lower mass density for its NS than those of the other known kHz QPO sources, with a radius range of 17–20 km, which excludes the strange quark matter inside its star.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 3
    Publication Date: 2013-04-26
    Description: After 2010, three outbursts of H1743–322 were detected by RXTE . We have carried out timing and spectral analysis of the data, emphasizing on the two with relatively complete evolution history presented in the RXTE /Proportional Counter Array observations. We then constitute an enlarged outburst sample for H1743–322 which allows us to investigate the spectral transitions in more details. We find that the spectral transitions to high-soft state constrain a region for four outbursts in hardness–intensity diagram. An extension of the region locates in the vicinity of the failed outburst in 2008, and excludes it from a successful group. We therefore suggest that the failed outburst in 2008 may present the first almost successful outburst sample, which is important for modelling the outburst, especially upon the conditions required for transition to high-soft state.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 4
    Publication Date: 2015-05-12
    Description: Motivation: The probability of effective treatment of cancer with a targeted therapeutic can be improved for patients with defined genotypes containing actionable mutations. To this end, many human cancer biobanks are integrating more tightly with genomic sequencing facilities and with those creating and maintaining patient-derived xenografts (PDX) and cell lines to provide renewable resources for translational research. Results: To support the complex data management needs and workflows of several such biobanks, we developed Acquire. It is a robust, secure, web-based, database-backed open-source system that supports all major needs of a modern cancer biobank. Its modules allow for i) up-to-the-minute ‘scoreboard’ and graphical reporting of collections; ii) end user roles and permissions; iii) specimen inventory through caTissue Suite; iv) shipping forms for distribution of specimens to pathology, genomic analysis and PDX/cell line creation facilities; v) robust ad hoc querying; vi) molecular and cellular quality control metrics to track specimens’ progress and quality; vii) public researcher request; viii) resource allocation committee distribution request review and oversight and ix) linkage to available derivatives of specimen. Availability and Implementation: Acquire implements standard controlled vocabularies, ontologies and objects from the NCI, CDISC and others. Here we describe the functionality of the system, its technological stack and the processes it supports. A test version Acquire is available at https://tcrbacquire-stg.research.bcm.edu ; software is available in https://github.com/BCM-DLDCC/Acquire ; and UML models, data and workflow diagrams, behavioral specifications and other documents are available at https://github.com/BCM-DLDCC/Acquire/tree/master/supplementaryMaterials . Contact: becnel@bcm.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 5
    Publication Date: 2016-04-08
    Description: Congenital heart disease (CHD) is the most common developmental abnormality, and is the leading noninfectious cause of mortality in neonates. Increasing evidence demonstrates that genetic defects play an important role in the pathogenesis of CHD. However, CHD exhibits substantial heterogeneity, and the genetic determinants for CHD remain unknown in the overwhelming majority of cases. In the current study, the coding exons and flanking introns of the HAND2 gene, which encodes a basic helix-loop-helix transcription factor essential for normal cardiovascular development, were sequenced in 192 unrelated patients with CHD, and a novel heterozygous mutation, p.S65I, was identified in a patient with congenital ventricular septal defect (VSD). Genetic analysis of the index patient’s pedigree revealed that the mutation was present in all seven affected family members available, but absent in the 13 unaffected family members examined. Besides, in addition to VSD, five of the proband’s close relatives also had pulmonary stenosis (PS), and the proband’s son also had double outlet right ventricle (DORV). The missense mutation, which altered an evolutionarily conserved amino acid, was absent in 300 unrelated, ethnically matched healthy individuals. Biological analyses using a dual-luciferase reporter assay system showed that the mutant HAND2 was associated with significantly diminished transcriptional activity. Furthermore, the mutation abolished the synergistic activation between HAND2 and GATA4, as well as NKX2.5—two other cardiac core transcriptional factors that have been causally linked to CHD. These findings indicate that HAND2 loss-of-function mutation contributes to human CHD, perhaps via its interaction with GATA4 and NKX2.5.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 6
    Publication Date: 2014-11-28
    Description: Nucleic acids have become a powerful tool in nanotechnology because of their controllable diverse conformational transitions and adaptable higher-order nanostructure. Using single-stranded DNA probes as the pore-caps for various target recognition, here we present an ultrasensitive universal electrochemical detection system based on graphene and mesoporous silica, and achieve sensitivity with all of the major classes of analytes and simultaneously realize DNA logic gate operations. The concept is based on the locking of the pores and preventing the signal-reporter molecules from escape by target-induced the conformational change of the tailored DNA caps. The coupling of ‘waking up’ gatekeeper with highly specific biochemical recognition is an innovative strategy for the detection of various targets, able to compete with classical methods which need expensive instrumentation and sophisticated experimental operations. The present study has introduced a new electrochemical signal amplification concept and also adds a new dimension to the function of graphene-mesoporous materials hybrids as multifunctional nanoscale logic devices. More importantly, the development of this approach would spur further advances in important areas, such as point-of-care diagnostics or detection of specific biological contaminations, and hold promise for use in field analysis.
    Keywords: Phsyical and Biochemical Characterisation of DNA
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
    Publication Date: 2012-08-29
    Description: Sustained Toll-like receptor (TLR) stimulation continuously activates antimicrobial genes but paradoxically represses inflammatory genes. This phenomenon, termed TLR tolerance, is essential for preventing fatal inflammatory conditions such as sepsis, but its underlying mechanisms are unclear. We report here that NF-κB binding nucleic acids of gene promoters are tolerogenic motifs, which...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 8
    Publication Date: 2012-09-13
    Description: A new strategy to create site-specific, homogeneous, and bright silver nanoclusters (AgNCs) with high-stability was demonstrated by triplex DNA as template. By reasonable design of DNA sequence, homogeneous Ag 2 cluster was obtained in the predefined position of CG.C + site of triplex DNA. This strategy was also explored for controlled alignment of AgNCs on the DNA nanoscaffold. To the best of our knowledge, this was the first example to simultaneously answer the challenges of excellent site-specific nucleation and growth, homogeneity and stability against salt of DNA-templated AgNCs.
    Keywords: Nucleic acid structure
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 9
    Publication Date: 2012-09-13
    Description: There is great interest in design and synthesis of small molecules which selectively target specific genes to inhibit biological functions in which particular DNA structures participate. Among these studies, chiral recognition has been received much attention because more evidences have shown that conversions of the chirality and diverse conformations of DNA are involved in a series of important life events. Here, we report that a pair of chiral helical macrocyclic lanthanide (III) complexes, ( M )-Yb[L SSSSSS ] 3+ and ( P )-Yb[L RRRRRR ] 3+ , can enantioselectively bind to B-form DNA and show remarkably contrasting effects on GC-rich and AT-rich DNA. Neither of them can influence non-B-form DNA, nor quadruplex DNA stability. Our results clearly show that P-enantiomer stabilizes both poly(dG-dC) 2 and poly(dA-dT) 2 while M-enantiomer stabilizes poly(dA-dT) 2 , however, destabilizes poly(dG-dC) 2 . To our knowledge, this is the best example of chiral metal compounds with such contrasting preference on GC- and AT-DNA. Ligand selectively stabilizing or destabilizing DNA can interfere with protein–DNA interactions and potentially affect many crucial biological processes, such as DNA replication, transcription and repair. As such, bearing these unique capabilities, the chiral compounds reported here may shed light on the design of novel enantiomers targeting specific DNA with both sequence and conformation preference.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 10
    Publication Date: 2014-10-03
    Description: Severe influenza A(H1N1)pdm09 infection induces thymic atrophy through activating innate CD8+CD44hi T cells by upregulating IFN-γ Cell Death and Disease 5, e1440 (October 2014). doi:10.1038/cddis.2014.323 Authors: B Liu, X Zhang, W Deng, J Liu, H Li, M Wen, L Bao, J Qu, Y Liu, F Li, Y An, C Qin, B Cao & C Wang
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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