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  • 1
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    New model to explain tooth wear [Anthropology] (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-08-26
    Description: Paleoanthropologists and vertebrate paleontologists have for decades debated the etiology of tooth wear and its implications for understanding the diets of human ancestors and other extinct mammals. The debate has recently taken a twist, calling into question the efficacy of dental microwear to reveal diet. Some argue that endogenous abrasives...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    Improving compound-protein interaction prediction by building up highly credible negative samples (2015)
    Oxford University Press
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    Publication Date: 2015-06-14
    Description: Motivation: Computational prediction of compound–protein interactions (CPIs) is of great importance for drug design and development, as genome-scale experimental validation of CPIs is not only time-consuming but also prohibitively expensive. With the availability of an increasing number of validated interactions, the performance of computational prediction approaches is severely impended by the lack of reliable negative CPI samples. A systematic method of screening reliable negative sample becomes critical to improving the performance of in silico prediction methods. Results: This article aims at building up a set of highly credible negative samples of CPIs via an in silico screening method. As most existing computational models assume that similar compounds are likely to interact with similar target proteins and achieve remarkable performance, it is rational to identify potential negative samples based on the converse negative proposition that the proteins dissimilar to every known/predicted target of a compound are not much likely to be targeted by the compound and vice versa. We integrated various resources, including chemical structures, chemical expression profiles and side effects of compounds, amino acid sequences, protein–protein interaction network and functional annotations of proteins, into a systematic screening framework. We first tested the screened negative samples on six classical classifiers, and all these classifiers achieved remarkably higher performance on our negative samples than on randomly generated negative samples for both human and Caenorhabditis elegans . We then verified the negative samples on three existing prediction models, including bipartite local model, Gaussian kernel profile and Bayesian matrix factorization, and found that the performances of these models are also significantly improved on the screened negative samples. Moreover, we validated the screened negative samples on a drug bioactivity dataset. Finally, we derived two sets of new interactions by training an support vector machine classifier on the positive interactions annotated in DrugBank and our screened negative interactions. The screened negative samples and the predicted interactions provide the research community with a useful resource for identifying new drug targets and a helpful supplement to the current curated compound–protein databases. Availability: Supplementary files are available at: http://admis.fudan.edu.cn/negative-cpi/ . Contact: sgzhou@fudan.edu.cn 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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    A free-form mass model of the Hubble Frontier Fields cluster AS1063 (RXC J2248.7-4431) with over one hundred constraints (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-12
    Description: We derive a free-form mass distribution for the massive cluster AS1063 ( z = 0.348) using the completed optical imaging from the Hubble Frontier Fields programmme. Based on a subset of 11 multiply lensed systems with spectroscopic redshift, we produce a lens model that is accurate enough to secure new multiply lensed systems, totalling over a 100 arclets, and to estimate their redshifts geometrically. Consistency is found between this precise model and that obtained using only the subset of lensed sources with spectroscopically measured redshifts. Although a relatively large elongation of the mass distribution is apparent relative to the X-ray map, no significant offset is found between the centroid of our mass distribution and that of the X-ray emission map, suggesting a relatively relaxed state for this cluster. For the well-resolved lensed images, we provide detailed model comparisons to illustrate the precision of our model and hence the reliability of our de-lensed sources. A clear linear structure is associated with one such source extending 23 kpc in length, that could be an example of jet-induced star formation, at redshift z 3.1.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    On the origin of the soft photons of the high-synchrotron-peaked blazar PKS 1424+240 (2016)
    Oxford University Press
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    Publication Date: 2016-07-09
    Description: PKS 1424+240 is a distant very-high-energy gamma-ray BL Lac object with redshift z  = 0.601. It has been found that models utilizing pure synchrotron self-Compton (SSC) processes normally need extreme input parameters (e.g. a very low magnetic field intensity and an extraordinarily high Doppler factor) to explain this particular object spectral energy distributions (SEDs). In order to avoid these extreme model parameters, various other models have been proposed (e.g. the two-zone SSC model or lepto-hadronic model). In this work, we employ the traditional one-zone leptonic model after including a weak external Compton component in order to explore the simultaneous multiwavelength SEDs of PKS 1424+240 in both the high (2009) and the low (2013) state. We find that the input parameters of the magnetic field and Doppler factor are roughly consistent with those of other BL Lacs if a weak external photon field from either the broad line region (BLR) or the dust torus is assumed. However, the required energy density of seed photons from the BLR or torus is about three orders of magnitude lower than that the energy density estimated from the observations in luminous quasars (e.g. flat-spectrum radio quasars, FSRQs). This result suggests that the BLR/torus in BL Lacs is much weaker than that of luminous FSRQs (but has not fully disappeared), and that the inverse-Compton process of external photons from the BLR/torus may still play a role even in high-synchrotron-peaked blazars.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Biochemistry and application of a TET-like protein [Biochemistry] (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-04-08
    Description: Modified DNA bases in mammalian genomes, such as 5-methylcytosine (5mC) and its oxidized forms, are implicated in important epigenetic regulation processes. In human or mouse, successive enzymatic conversion of 5mC to its oxidized forms is carried out by the ten-eleven translocation (TET) proteins. Previously we reported the structure of a...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Field homogeneity improvement of maglev NdFeB magnetic rails from joints (2016)
    SpringerOpen
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    Publication Date: 2016-03-26
    Description: An ideal magnetic rail should provide a homogeneous magnetic field along the longitudinal direction to guarantee the reliable friction-free operation of high temperature superconducting (HTS) maglev vehicles. ...
    Electronic ISSN: 2193-1801
    Topics: Natural Sciences in General
    Published by SpringerOpen
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  • 7
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    Strontium, Sulfur, Carbon, and Oxygen Isotope Geochemistry of the Early Cambrian Strata-bound Barite and Witherite Deposits of the Qinling-Daba Region, Northern Margin of the Yangtze Craton, China (2016)
    Society of Economic Geologists (SEG)
    Details
    Publication Date: 2016-04-09
    Description: Early Cambrian black shale and chert in the Qinling-Daba region along the northern margin of the Yangtze (South China) craton host important high-grade strata-bound barite and witherite deposits. Barite-dominated deposits occur in a northern thrust domain, whereas witherite-dominated deposits occur in a thrust domain a few tens of km to the southwest. The authors studied the strontium isotope ( 87 Sr/ 86 Sr), and stable isotope composition ( 34 S, 13 C, and 18 O) of barite and witherite from the Shenxiantai and Chiyan deposits, two representative Ba deposits in the region, and compared these data to previously reported Sr, S, C, and O isotope data on a variety of Ba deposits in a similar stratigraphic position along the Early Cambrian rifted margin of the Yangtze craton. Most barite and witherite deposits in the Qinling-Daba region have consistent 87 Sr/ 86 Sr ratios with an average value of 0.70845 ± 0.00017 (1 , n = 53), in the range of Early Cambrian seawater from 0.7081 to 0.7090. Barite 34 S and 18 O VSMOW values vary from 8.0 to 76.1 (avg 40.6 ± 13.2, 1 , n = 35) and from 9.9 to 24.7 (avg 19.0 ± 3.0, 1 , n = 103), respectively, generally higher than those of seawater sulfate in the Early Cambrian. We propose that seawater-derived barium was precipitated in the anoxic water column and during early diagenesis. Bacterial sulfate reduction (BSR) and reoxidation under partial sulfate limitation produced higher 34 S and 18 O values of the diagenetic barite compared to contemporaneous seawater sulfate. The 13 C values of Ba carbonate minerals (witherite and barytocalcite) vary from –10.8 to –23.6 (avg –14.1 ± 3.2, 1 , n = 84) and indicate the involvement of carbon from oxidized organic matter. Although the 87 Sr/ 86 Sr ratios, 34 S, and 13 C values of barite and witherite are very close, barite has slightly higher 18 O VSMOW values (avg 22.0 ± 1.6, 1 , n = 19) than witherite and barytocalcite (avg 18.0 ± 2.5, 1 , n = 84), possibly revealing the role of CO 2 -rich cold seeps under sulfate-limited sedimentary-diagenetic conditions during the formation of the witherite-dominated deposits. The Sr isotope composition of barite in the Shenxiantai deposit is different from the other barite deposits and has lower 87 Sr/ 86 Sr ratios, which suggests the involvement of less radiogenic Sr in diagenetic fluids which interacted with underlying mafic volcanic rocks.
    Print ISSN: 0361-0128
    Topics: Geosciences
    Published by Society of Economic Geologists (SEG)
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  • 8
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    Study of toroidal flow generation by ion cyclotron range of frequency minority heating in the Alcator C-Mod plasma (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-01-05
    Description: The averaged toroidal flow of energetic minority ions during ICRF (ion cyclotron range of frequencies) heating is investigated in the Alcator C-Mod plasma by applying the GNET code, which can solve the drift kinetic equation with complicated orbits of accelerated energetic particles. It is found that a co-directional toroidal flow of the minority ions is generated in the region outside of the resonance location, and that the toroidal velocity reaches more than 40% of the central ion thermal velocity ( V tor ∼ 300 km/s with P ICRF ∼ 2 MW). When we shift the resonance location to the outside of | r / a | ∼ 0.5 , the toroidal flow immediately inside of the resonance location is reduced to 0 or changes to the opposite direction, and the toroidal velocity shear is enhanced at r / a ∼ 0.5. A radial diffusion equation for toroidal flow is solved by assuming a torque profile for the minority ion mean flow, and good agreements with experimental radial toroidal flow profiles are obtained. This suggests that the ICRF driven minority ion flow is related to the experimentally observed toroidal rotation during ICRF heating in the Alcator C-Mod plasma.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 9
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    Suramin targets cullin [Biochemistry] (2016)
    National Academy of Sciences
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    Publication Date: 2016-04-06
    Description: Cullin-RING E3 ubiquitin ligases (CRL) control a myriad of biological processes by directing numerous protein substrates for proteasomal degradation. Key to CRL activity is the recruitment of the E2 ubiquitin-conjugating enzyme Cdc34 through electrostatic interactions between E3′s cullin conserved basic canyon and the acidic C terminus of the E2 enzyme....
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    Bright and photostable chemigenetic indicators for extended in vivo voltage imaging (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉Genetically encoded voltage indicators (GEVIs) enable monitoring of neuronal activity at high spatial and temporal resolution. However, the utility of existing GEVIs has been limited by the brightness and photostability of fluorescent proteins and rhodopsins. We engineered a GEVI, called Voltron, that uses bright and photostable synthetic dyes instead of protein-based fluorophores, thereby extending the number of neurons imaged simultaneously in vivo by a factor of 10 and enabling imaging for significantly longer durations relative to existing GEVIs. We used Voltron for in vivo voltage imaging in mice, zebrafish, and fruit flies. In the mouse cortex, Voltron allowed single-trial recording of spikes and subthreshold voltage signals from dozens of neurons simultaneously over a 15-minute period of continuous imaging. In larval zebrafish, Voltron enabled the precise correlation of spike timing with behavior.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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