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  • 1
    Publication Date: 2016-07-09
    Description: Epistasis plays an essential role in the development of complex diseases. Interaction methods face common challenge of seeking a balance between persistent power, model complexity, computation efficiency, and validity of identified bio-markers. We introduce a novel W-test to identify pairwise epistasis effect, which measures the distributional difference between cases and controls through a combined log odds ratio. The test is model-free, fast, and inherits a Chi-squared distribution with data adaptive degrees of freedom. No permutation is needed to obtain the P -values. Simulation studies demonstrated that the W-test is more powerful in low frequency variants environment than alternative methods, which are the Chi-squared test, logistic regression and multifactor-dimensionality reduction (MDR). In two independent real bipolar disorder genome-wide associations (GWAS) datasets, the W-test identified significant interactions pairs that can be replicated, including SLIT3-CENPN, SLIT3-TMEM132D, CNTNAP2-NDST4 and CNTCAP2-RTN4R . The genes in the pairs play central roles in neurotransmission and synapse formation. A majority of the identified loci are undiscoverable by main effect and are low frequency variants. The proposed method offers a powerful alternative tool for mapping the genetic puzzle underlying complex disorders.
    Keywords: Polymorphism/mutation detection
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉HY-2A is China's first satellite altimeter mission, launched in Aug. 2011. Its geodetic mission (GM) started from 2016 March 30 till present, collecting sea surface heights for about five 168-d cycles. To test how the HY-2A altimeter performs in marine gravity derivation, we use the least-squares collocation method to determine marine gravity anomalies on 1′ × 1′ grids around the South China Sea (covering 0°–30°N, 105°E–125°E) from the HY-2A/GM-measured geoid gradients. We assess the qualities of the HY-2A/GM-derived gravity over different depths and areas using the bias and tilt-adjusted ship-borne gravity anomalies from the U.S. National Centers for Environmental Information (NCEI) and the Second Institute of Oceanography, Ministry of Natural Resources (MNR) of P. R. China. The RMS difference between the HY-2A/GM-derived and the NCEI ship-borne gravity is 5.91 mGal, and is 5.33 mGal when replacing the HY-2A value from the Scripps Institution of Oceanography (SIO) V23.1 value. The RMS difference between the HY-2A/GM-derived and the MNR ship-borne gravity is 2.90 mGal, and is 2.76 mGal when replacing the HY-2A value from the SIO V23.1 value. The RMS difference between the HY-2A and SIO V23.1 value is 3.57 mGal in open sea areas at least 20 km far away from the coast. In general, the difference between the HY-2A/GM-derived gravity and ship-borne gravity decreases with decreasing gravity field roughness and increasing depth. HY-2A results in the lowest gravity accuracy in areas with islands or reefs. Our assessment result suggests that HY-2A can compete with other Ku-band altimeter missions in marine gravity derivation.〈/span〉
    Print ISSN: 2051-1965
    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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  • 3
    Publication Date: 2015-10-16
    Description: Here we present a catalogue of 1056 spectroscopically identified hydrogen-dominated white dwarfs (DAWDs), 34 helium-dominated white dwarfs (DBWDs) and 276 white dwarf main sequence (WDMS) binaries from the Large sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) survey data release 2 (DR2). 383 DAWDs, 4 DBWDs and 138 WDMSs are new identifications after cross-match with literature. There are ~4100 k spectra in total from DR 2. The low ratio of white dwarfs found in LAMOST is attributed to biased selection of LAMOST input catalogue and much brighter targets relative to stars observed in Sloan Digital Sky Survey. In this paper, a new DAWD selection method is adopted as a new attempt and supplement to the traditional methods. The effective temperature, surface gravity, mass, cooling age and distance of high signal-to-noise DAWDs are estimated. The peak of the mass distribution is found to be ~0.6 M , which is consistent with previous work. The parameters of WDMS binaries are also provided in this paper. As the foundation of our future work, which is to identify more WDs with debris disc, WDs found in LAMOST showed a lot of potential. Interesting infrared-excess WDs will be reported in our forthcoming paper.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 4
    Publication Date: 2015-10-25
    Description: A new approach based on energy conservation principle for satellite gravimetry mission has been developed and yields more accurate estimation of in situ geopotential difference observables using K-band ranging (KBR) measurements from the Gravity Recovery and Climate Experiment (GRACE) twin-satellite mission. This new approach preserves more gravity information sensed by KBR range-rate measurements and reduces orbit error as compared to previous energy balance methods. Results from analysis of 11 yr of GRACE data indicated that the resulting geopotential difference estimates agree well with predicted values from official Level 2 solutions: with much higher correlation at 0.9, as compared to 0.5–0.8 reported by previous published energy balance studies. We demonstrate that our approach produced a comparable time-variable gravity solution with the Level 2 solutions. The regional GRACE temporal gravity solutions over Greenland reveals that a substantially higher temporal resolution is achievable at 10-d sampling as compared to the official monthly solutions, but without the compromise of spatial resolution, nor the need to use regularization or post-processing.
    Keywords: Gravity, Geodesy and Tides
    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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  • 5
    Publication Date: 2015-10-22
    Description: To investigate the coupling relationship between great earthquake and ionosphere, the GPS-derived total electron contents (TECs) by the Center for Orbit Determination in Europe and the foF2 data from the Space Weather Prediction Center were used to analyse the impending ionospheric anomalies before the Iquique Mw8.2 earthquake in Chile on 2014 April 1. Eliminating effects of the solar and geomagnetic activities on ionosphere by the sliding interquartile range with the 27-day window, the TEC analysis results represent that there were negative anomalies occurred on 15th day prior to the earthquake, and positive anomalies appeared in 5th day before the earthquake. The foF2 analysis results of ionosonde stations Jicamarca, Concepcion and Ramey show that the foF2 increased by 40, 50 and 45 per cent, respectively, on 5th day before the earthquake. The TEC anomalous distribution indicates that there was a widely TEC decrement over the epicentre with the duration of 6 hr on 15th day before the earthquake. On 5th day before the earthquake, the TEC over the epicentre increased with the amplitude of 15 TECu, and the duration exceeded 6 hr. The anomalies occurred on the side away from the equator. All TEC anomalies in these days were within the bounds of equatorial anomaly zone where should be the focal area to monitor ionospheric anomaly before strong earthquakes. The relationship between ionospheric anomalies and geomagnetic activity was detected by the cross wavelet analysis, which implied that the foF2 was not affected by the magnetic activities on 15th day and 5th day prior to the earthquake, but the TECs were partially affected by anomalous magnetic activity during some periods of 5th day prior to the earthquake.
    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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  • 6
    Publication Date: 2016-06-16
    Description: Transcription factors (TFs) regulate gene expression through binding to specific target DNA sites. Accurate annotation of transcription factor binding sites (TFBSs) at genome scale represents an essential step toward our understanding of gene regulation networks. In this article, we present a structure-based method for computational prediction of TFBSs using a novel, integrative energy (IE) function. The new energy function combines a multibody (MB) knowledge-based potential and two atomic energy terms (hydrogen bond and interaction) that might not be accurately captured by the knowledge-based potential owing to the mean force nature and low count problem. We applied the new energy function to the TFBS prediction using a non-redundant dataset that consists of TFs from 12 different families. Our results show that the new IE function improves the prediction accuracy over the knowledge-based, statistical potentials, especially for homeodomain TFs, the second largest TF family in mammals. Contact: jguo4@uncc.edu 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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  • 7
    Publication Date: 2015-07-16
    Description: This paper is concerned with the inverse scattering problem of time-harmonic acoustic plane waves by a crack buried in a piecewise homogeneous medium. We first show the well-posedness of the solution to the direct problem by using the boundary integral method. Then a uniqueness result for the inverse problem is obtained, that is, the shape of the crack and the surface parameter can be uniquely determined by the far-field pattern. The proof of the uniqueness result is based on a generalization of the mixed reciprocity relation. In particular, a mathematical basis is given to retrieve the shape of the crack by using the linear sampling method and difficulties arise from the fact that the crack has an empty interior.
    Print ISSN: 0272-4960
    Electronic ISSN: 1464-3634
    Topics: Mathematics
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  • 8
    Publication Date: 2012-11-09
    Description: In this paper, using lithium chloride and calcium chloride as modifying agents, the modified silica gel and molecular sieve composite based on ceramic fiber was prepared by treating ceramic fiber paper with sequential impregnation of the suspension of waterglass and molecular sieve and the aqueous solution of salt. The composition of the modified composite was characterized by using Fourier transform infrared spectroscopy (FTIR). Thermogravimetry (TG) and temperature programmed desorption (TPD) were used to evaluate the desorption performance of the composite. FTIR spectra indicated that impregnation salt has no effect on the composition of molecular sieve. TG and TPD analysis indicated that desorption activated energy of modified composite was lower than that of molecular sieve. The result of the dynamic and static adsorption experiment showed that the adsorption performance of molecular sieve enhanced greatly through the modification.
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 9
    Publication Date: 2012-06-16
    Description: In this paper, we discuss the use of some representation results for double martingales to value and hedge contingent claims in a Markovian regime-switching market. A set of N Markov jump assets is introduced to complete the Markovian regime-switching market. Using a representation for double martingales, we justify the completeness of the enlarged market. An equivalent martingale measure, or price kernel, in the enlarged market is then identified by a measure change. The option pricing formula and the hedging portfolio in the enlarged market is also discussed.
    Print ISSN: 1471-678X
    Electronic ISSN: 1471-6798
    Topics: Mathematics
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  • 10
    Publication Date: 2015-04-03
    Description: Motivation: Transcriptional regulatory networks controlling cell fate decisions in mammalian embryonic development remain elusive despite a long time of research. The recent emergence of single-cell RNA profiling technology raises hope for new discovery. Although experimental works have obtained intriguing insights into the mouse early development, a holistic and systematic view is still missing. Mathematical models of cell fates tend to be concept-based, not designed to learn from real data. To elucidate the regulatory mechanisms behind cell fate decisions, it is highly desirable to synthesize the data-driven and knowledge-driven modeling approaches. Results: We propose a novel method that integrates the structure of a cell lineage tree with transcriptional patterns from single-cell data. This method adopts probabilistic Boolean network (PBN) for network modeling, and genetic algorithm as search strategy. Guided by the ‘directionality’ of cell development along branches of the cell lineage tree, our method is able to accurately infer the regulatory circuits from single-cell gene expression data, in a holistic way. Applied on the single-cell transcriptional data of mouse preimplantation development, our algorithm outperforms conventional methods of network inference. Given the network topology, our method can also identify the operational interactions in the gene regulatory network (GRN), corresponding to specific cell fate determination. This is one of the first attempts to infer GRNs from single-cell transcriptional data, incorporating dynamics of cell development along a cell lineage tree. Availability and implementation: Implementation of our algorithm is available from the authors upon request. Contact: zhengjie@ntu.edu.sg 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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