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  • 1
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    Regional pattern of Bosmina responses to fish introduction and eutrophication in four large lakes from Southwest China (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-04
    Description: Fish introduction and nutrient enrichment are two major environmental stressors for many freshwater lakes. Thus far, their ecological impacts have largely been evaluated independently, despite that fish invasion and predation may interact with lake trophic status. We examined paleoecological records from four large lakes of Southwest China to quantify the strength and interaction of icefish invasion and eutrophication in affecting zooplankton over time. There was a significant and positive relationship ( P 〈 0.01) between sediment Chl a concentration and bosminid flux in each lake with bosminid size structure being greater in more productive lakes, indicating a strong bottom-up control. Furthermore, a consistent decrease in bosminid body sizes after fish introduction was found in Fuxian where icefish grew most successfully among our lakes. The variance partitioning results showed a decrease in the relative importance of planktivorous predation in driving zooplankton production with increased trophic status across lakes, with their joint effect showing a unimodal model in strength. In all, there was regional heterogeneity in the population status and ecological impact of invasive icefish that varied with lake trophic status over time. Therefore, nutrient status needs to be considered in assessing long-term ecological status and consequences of fish invasion in stressed freshwaters.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Automated profiling of individual cell-cell interactions from high-throughput time-lapse imaging microscopy in nanowell grids (TIMING) (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-22
    Description: Motivation: There is a need for effective automated methods for profiling dynamic cell–cell interactions with single-cell resolution from high-throughput time-lapse imaging data, especially, the interactions between immune effector cells and tumor cells in adoptive immunotherapy. Results: Fluorescently labeled human T cells, natural killer cells (NK), and various target cells (NALM6, K562, EL4) were co-incubated on polydimethylsiloxane arrays of sub-nanoliter wells (nanowells), and imaged using multi-channel time-lapse microscopy. The proposed cell segmentation and tracking algorithms account for cell variability and exploit the nanowell confinement property to increase the yield of correctly analyzed nanowells from 45% (existing algorithms) to 98% for wells containing one effector and a single target, enabling automated quantification of cell locations, morphologies, movements, interactions, and deaths without the need for manual proofreading. Automated analysis of recordings from 12 different experiments demonstrated automated nanowell delineation accuracy 〉99%, automated cell segmentation accuracy 〉95%, and automated cell tracking accuracy of 90%, with default parameters, despite variations in illumination, staining, imaging noise, cell morphology, and cell clustering. An example analysis revealed that NK cells efficiently discriminate between live and dead targets by altering the duration of conjugation. The data also demonstrated that cytotoxic cells display higher motility than non-killers, both before and during contact. Contact : broysam@central.uh.edu or nvaradar@central.uh.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
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  • 3
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    Polymorphisms and haplotypes of the miR-148/152 family are associated with the risk and clinicopathological features of gastric cancer in a Northern Chinese population (2014)
    Oxford University Press
    Details
    Publication Date: 2014-10-19
    Description: Our previous studies showed that the expressions of miR-148a, miR-152 and miR-148b are altered in gastric cancer (GC). The present study aimed to find relationship between individual single nucleotide polymorphisms (SNPs) or haplotypes of these miRNAs and susceptibility, clinicopathological parameters and prognosis of GC in a large sample of the Han population of Northern China. Twelve SNPs were genotyped using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry in a case–control study of 571 Chinese GC patients and 571 cancer-free controls. The rs11170877 G allele ( P = 0.027) and the rs12231393 C allele ( P = 0.034) were associated with a decreased risk of GC. However, these associations were lost after Bonferroni correction. The rs4719839 G allele was associated with Borrmann type III–IV GC ( P = 0.034), increased tumour size ( P = 0.020), an increased rate of lymph node metastasis ( P = 0.047) and advanced TNM stage ( P = 0.009). These associations were also lost after Bonferroni correction. The haplotype of miR-148b was significantly correlated with GC risk. The haplotypes in miRNA-148a were different in Borrmann types. The haplotype of miR-152 distributed various in the positive lymphovascular invasion group compared to negative group. Polymorphisms of miR-148b rs11170877 and 12231393 and their haplotypes were predictive factors of susceptibility to GC. A functional genetic variant of miRNA rs4719839 and the corresponding haplotype were associated with clinicopathological features and prognosis of advanced GCs.
    Print ISSN: 0267-8357
    Electronic ISSN: 1464-3804
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 4
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    Reproducing the spectral energy distribution of PKS 1424+240: the role of automatic photon quenching (2016)
    Oxford University Press
    Details
    Publication Date: 2016-10-28
    Description: We present a one-zone homogeneous self-consistent model for the multiwavelength emission features of PKS 1424+240 that allows the effects of automatic photon quenching to be studied. In the model, a steady -ray injection rate in the source is assumed and the non-linear time-dependent kinematic equations describing the evolution of both electrons and photons are then acquired; these self-consistently involve photon–photon interaction, synchrotron radiation of electron/positron pairs, inverse Compton scattering and synchrotron self-absorption. The model is applied to reproduce the multiwavelength spectrum of PKS 1424+240; our results indicate that the observed spectral energy distribution (SED) of PKS 1424+240 can be reproduced well in the case of both electron injection and photon injection. The injected electrons mainly influence the SED over radio, optical and X-ray bands and the SED in the high-energy -ray band is determined mainly by automatic photon quenching; in particular, the break form of the spectrum in the energy range ≥ a few GeV is caused by this. It should be noted that the observed SED from X-ray to -ray bands can be reproduced only through quenching, provided the observed data in the optical band are produced through some other mechanism, e.g. electron synchrotron radiation.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    A new dust budget in the Large Magellanic Cloud (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-07
    Description: The origin of dust in a galaxy is poorly understood. Recently, surveys of the Large Magellanic Cloud (LMC) have provided astrophysical laboratories for dust studies. Using a method of population synthesis, we investigate the contributions of dust produced by asymptotic giant branch (AGB) stars, common envelope (CE) ejecta and Type II supernovae (SNe II) to the total dust budget in the LMC. Based on our models, the dust production rates (DPRs) of AGB stars in the LMC are between about 2.5 10 –5 and 4.0 10 –6 M yr –1 . The uncertainty mainly results from different models for the dust yields of AGB stars. The DPRs of CE ejecta are about 6.3 10 –6 (the initial binary fraction is 50 per cent). These results are within the large scatter of several observational estimates. AGB stars mainly produce carbon grains, which is consistent with observations. Most of the dust grains manufactured by CE ejecta are silicate and iron grains. The contributions of SNe II are very uncertain. Compared with SNe II without reverse shock, the DPRs of AGB stars and CE ejecta are negligible. However, if only 2 per cent of dust grains produced by SNe II can survive after reverse shock, the contributions of SNe II are very small. The total dust masses produced by AGB stars in the LMC are between 2.8 10 4 and 3.2 10 5 M , and those produced by CE ejecta are about 6.3 10 4 . They are much lower than the values estimated by observations. Therefore, there should be other dust sources in the LMC.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Splitting lemmas for the Finsler energy functional on the space of H1-curves (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-09
    Description: We establish the splitting lemmas (or generalized Morse lemmas) for the energy functionals of Finsler metrics on the natural Hilbert manifolds of $H^1$ -curves around a critical point or a critical $ {\mathbb R}^1$ orbit of a Finsler isometry-invariant closed geodesic. They are the desired generalization on Finsler manifolds of the corresponding Gromoll–Meyer's splitting lemmas on Riemannian manifolds [Gromoll and Meyer, ‘On differentiable functions with isolated critical points’, Topology 8 (1969) 361–369; Gromoll and Meyer ‘Periodic geodesics on compact Riemannian manifolds’, J. Differential Geom. 3 (1969) 493–510]. As an application, we extend to Finsler manifolds a result by Grove and Tanaka [‘On the number of invariant closed geodesics’, Acta Math. 140 (1978) 33–48; Tanaka, ‘On the existence of infinitely many isometry-invariant geodesics’, J. Differential Geom. 17 (1982) 171–184] about the existence of infinitely many, geometrically distinct, isometry invariant closed geodesics on a closed Riemannian manifold.
    Print ISSN: 0024-6115
    Electronic ISSN: 1460-244X
    Topics: Mathematics
    Published by Oxford University Press
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  • 7
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    DNA damage-induced activation of CUL4B targets HUWE1 for proteasomal degradation (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-20
    Description: The E3 ubiquitin ligase HUWE1/Mule/ARF-BP1 plays an important role in integrating/coordinating diverse cellular processes such as DNA damage repair and apoptosis. A previous study has shown that HUWE1 is required for the early step of DNA damage-induced apoptosis, by targeting MCL-1 for proteasomal degradation. However, HUWE1 is subsequently inactivated, promoting cell survival and the subsequent DNA damage repair process. The mechanism underlying its regulation during this process remains largely undefined. Here, we show that the Cullin4B-RING E3 ligase (CRL4B) is required for proteasomal degradation of HUWE1 in response to DNA damage. CUL4B is activated in a NEDD8-dependent manner, and ubiquitinates HUWE1 in vitro and in vivo . The depletion of CUL4B stabilizes HUWE1, which in turn accelerates the degradation of MCL-1, leading to increased induction of apoptosis. Accordingly, cells deficient in CUL4B showed increased sensitivity to DNA damage reagents. More importantly, upon CUL4B depletion, these phenotypes can be rescued through simultaneous depletion of HUWE1 , consistent with the role of CUL4B in regulating HUWE1. Collectively, these results identify CRL4B as an essential E3 ligase in targeting the proteasomal degradation of HUWE1 in response to DNA damage, and provide a potential strategy for cancer therapy by targeting HUWE1 and the CUL4B E3 ligase.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    A missing-link in the tectonic configuration of the Almacık Block along the North Anatolian Fault Zone (NW Turkey): Active faulting in the Bolu plain based on seismic reflection studies (2015)
    Oxford University Press
    Details
    Publication Date: 2015-04-17
    Description: The North Anatolian Fault Zone (NAFZ) starts to branch off in the western Bolu plain. The branches of the NAFZ in this location create the Almacık block which is surrounded by the latest surface ruptures of significant earthquakes that occurred between 1944 and 1999, but its northeastern part remains unruptured. The most recently formed rupture, that was a result of the 1999 November 12 Düzce earthquake, ended to the northwest of the Bakacak Fault. The connection between the Bakacak Fault and the main branch of the NAFZ via the Bolu plain has until now remained unknown. This paper establishes that the route of the missing link runs through the Dağkent, Kasaplar and Bürnük faults, a finding achieved with the help of seismic reflection studies. The paper also argues that the cross cutting nature of these newly determined faults and a stress analysis based on focal mechanism solutions of recent earthquakes demonstrate the termination of the suggested pull-apart nature of the Bolu plain.
    Keywords: Geodynamics and Tectonics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 9
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    A new dust budget in the Large Magellanic Cloud (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-12
    Description: The origin of dust in a galaxy is poorly understood. Recently, surveys of the Large Magellanic Cloud (LMC) have provided astrophysical laboratories for dust studies. Using a method of population synthesis, we investigate the contributions of dust produced by asymptotic giant branch (AGB) stars, common envelope (CE) ejecta and Type II supernovae (SNe II) to the total dust budget in the LMC. Based on our models, the dust production rates (DPRs) of AGB stars in the LMC are between about 2.5 10 –5 and 4.0 10 –6 M yr –1 . The uncertainty mainly results from different models for the dust yields of AGB stars. The DPRs of CE ejecta are about 6.3 10 –6 (the initial binary fraction is 50 per cent). These results are within the large scatter of several observational estimates. AGB stars mainly produce carbon grains, which is consistent with observations. Most of the dust grains manufactured by CE ejecta are silicate and iron grains. The contributions of SNe II are very uncertain. Compared with SNe II without reverse shock, the DPRs of AGB stars and CE ejecta are negligible. However, if only 2 per cent of dust grains produced by SNe II can survive after reverse shock, the contributions of SNe II are very small. The total dust masses produced by AGB stars in the LMC are between 2.8 10 4 and 3.2 10 5 M , and those produced by CE ejecta are about 6.3 10 4 . They are much lower than the values estimated by observations. Therefore, there should be other dust sources in the LMC.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Population synthesis of millisecond X-ray pulsars (2015)
    Oxford University Press
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    Publication Date: 2015-10-09
    Description: As the evolutionary link between the radio millisecond pulsars and the low-mass X-ray binaries or intermediate-mass X-ray binaries, the millisecond X-ray pulsars (MSXPs) are important objects in testing theories of pulsar formation and evolution. In general, neutron stars in MSXPs can form via core collapse supernova (CC channel) of massive stars or accretion induced collapse (AIC channel) of an accreting ONeMg white dwarf, whose mass reaches the Chandrasekhar limit. Here, in addition to CC and AIC channels we also consider another channel, i.e. evolution induced collapse (EIC channel) of a helium star with mass between 1.4 and 2.5 M . Using a population synthesis code, we have studied MSXPs arising from three different evolutionary channels. We find that the Galactic birthrates of transient MSXPs and persistent MSXPs are about 0.7–1.4 x 10 –4  yr –1 . Our population synthesis calculations have shown that about 50–90 per cent of the MSXPs have undergone CC channel, about 10–40 per cent of them have undergone EIC channel, and the MSXPs via AIC channel are the least.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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