| 1. |
- Cheng, Shi-Ping, et al.
(author)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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In: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Journal article (peer-reviewed)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 2. |
- Grbic, Nedelko, et al.
(author)
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Blind signal separation using overcomplete subband representation
- 2001
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In: IEEE transactions on speech and audio processing. - : IEEE. - 1063-6676 .- 1558-2353. ; 9:5, s. 524-533
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Journal article (peer-reviewed)abstract
- This paper discusses a multirate filterbank-based extended infomax algorithm for real-world signal separation, i.e., convolved mixtures separation. Since convolution in the time domain corresponds to instantaneous mixing in the frequency domain, polyphase subband projection naturally becomes an efficient alternative to the Fourier transform based frequency domain approach. The online implementation proposed is featured by a simultaneous inverse channel identification in the frequency domain and signal filtering in the time domain. It is shown that an over-representation structure reduces aliasing between different bands and results in more accurate inverse channel estimates. Therefore, it provides better performance than the Fourier transform based structure in the measures of both separation and distortion. The performance limitation of the method is also evaluated in terms of the Wiener solution.
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| 3. |
- Grbic, Nedelko, et al.
(author)
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Performance Improvement of Multiple Array 3D Sonic Digitizer System via Calibration
- 1999
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Conference paper (peer-reviewed)abstract
- Multiple array 3D sonic digitizer system is a product made for measuring the geometric structure of an arbitrary object in three dimension. This paper gives a theoretical performance evaluation of the system. The Cramer-Rao Lower Bound of the parameter estimates of a linear segment is derived. In addition, the distortion effect caused by the time-delay bias, including rescaling, rotation and bending of the original object, is clarified. A simple method using a line segment is proposed to calibrate the bias term arised in the different parts of the system. Finally a simulation gives a numerical demonstration of the previous analysis and performance improvement of the suggested method.
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| 4. |
- Jia, Kai-Hua, et al.
(author)
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Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome
- 2021
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In: Horticulture Research. - : Oxford University Press (OUP). - 2052-7276 .- 2662-6810. ; 8:1
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Journal article (peer-reviewed)abstract
- Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.
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| 5. |
- Kristan, Matej, et al.
(author)
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The Sixth Visual Object Tracking VOT2018 Challenge Results
- 2019
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In: Computer Vision – ECCV 2018 Workshops. - Cham : Springer Publishing Company. - 9783030110086 - 9783030110093 ; , s. 3-53
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2018 is the sixth annual tracker benchmarking activity organized by the VOT initiative. Results of over eighty trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis and a “real-time” experiment simulating a situation where a tracker processes images as if provided by a continuously running sensor. A long-term tracking subchallenge has been introduced to the set of standard VOT sub-challenges. The new subchallenge focuses on long-term tracking properties, namely coping with target disappearance and reappearance. A new dataset has been compiled and a performance evaluation methodology that focuses on long-term tracking capabilities has been adopted. The VOT toolkit has been updated to support both standard short-term and the new long-term tracking subchallenges. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website (http://votchallenge.net).
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| 6. |
- Tao, Xiao-Jiao, et al.
(author)
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Behind Acoustic Doppler Current Profiler : Narrowband Volume Backscattering Signal Model, Analysis and Estimation
- 1999
-
Reports (other academic/artistic)abstract
- This report examines the statistical properties of the narrowband Doppler volume backscattering process and discusses its spectral centroid estimation problem. After clarifying the mechanism of both the finite duration Doppler effect and the continuously space-shifted integration process, the first two order time-varying statistics under a more general assumption, i.e. von Mises distribution, of random phase are derived. The generalization permits nonuniform phase tendency, which occurs in layered medium scattering. Based on the locally stationary process model, the evolutionary spectrum of the signal is derived where the variation of the backscattering strength enters as an amplitude modulation. On the contrary, the variation of the random phase distribution acts as both the amplitude modulation and the frequency modulation. The observability and the estimation of the average flow speed are discussed. It is shown that even under the homogeneous condition, the spectral centroid does not coincide with the aver age flow speed. Finally, a semiparametric spectral centroid estimation method, which simply contains an AR(2) model with its time-varying coefficients adapted by a wavelet shrinkage is proposed.
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| 7. |
- Tao, Xiao-Jiao, et al.
(author)
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Narrowband acoustic Doppler backscattering signal .I. Evolutionary Spectral Analysis
- 2002
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In: IEEE Transactions on Signal Processing. - 1053-587X. ; 50:11, s. 2644-2655
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Journal article (peer-reviewed)abstract
- This paper examines the statistical properties of the narrowband Doppler volume backscattering process and analyzes its evolutionary spectrum. After clarifying the mechanism of both the finite duration Doppler effect and the continuously space-shifted integration process, the first two order time-varying statistics under a more general assumption, i.e., von Mises distribution, of random phase are derived. The generalization permits nonuniform phase tendency, which occurs in layered medium scattering. Based on the locally stationary process model, the evolutionary spectrum of the signal is derived. It is shown that the variation of the backscattering strength enters the spectrum as an amplitude modulation, whereas the variation of the random phase distribution acts as both the amplitude modulation and the frequency modulation. Finally, the observability of the average flow speed using the spectral centroid estimate is discussed.
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| 8. |
- Tao, Xiao-Jiao, et al.
(author)
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Narrowband acoustic Doppler backscattering signal .II. Spectral Centroid estimation
- 2002
-
In: IEEE Transactions on Signal Processing. - 1053-587X. ; 50:11, s. 2656-2660
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Journal article (peer-reviewed)abstract
- For pt.I see ibid., vol.50, p.2644-2655 (2002). This paper proposes a novel algorithm to estimate the time-varying spectral centroid of the narrowband Doppler volume backscattering signal. It is constructed in a semi-parametric way, that is, modeling parametrically the local narrowband evolutionary spectrum using an AR(2) and nonparametrically adapting its time-varying coefficients using the wavelet shrinkage. The improved performance is gained by the underlying linear prediction function of the AR(2) and the minimax optimality of the unknown smoothness adaptation of the wavelet shrinkage procedure.
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| 9. |
- Tao, Xiao-Jiao, et al.
(author)
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Narrowband acoustic doppler volume backscattering signal-part I : evolutionary spectral analysis
- 2002
-
In: IEEE Transactions on Signal Processing. - 1053-587X .- 1941-0476. ; 50:11, s. 2644-2655
-
Journal article (peer-reviewed)abstract
- This paper examines the statistical properties of the narrowband Doppler volume backscattering process and analyzes its evolutionary spectrum. After clarifying the mechanism of both the finite duration Doppler effect and the continuously space-shifted integration process, the first two order time-varying statistics under a more general assumption, i.e., von Mises distribution, of random phase are derived. The generalization permits nonuniform phase tendency, which occurs in layered medium scattering. Based on the locally stationary process model, the evolutionary spectrum of the signal is derived. It is shown that the variation of the backscattering strength enters the spectrum as an amplitude modulation, whereas the variation of the random phase distribution acts as both the amplitude modulation and the frequency modulation. Finally, the observability of the average flow speed using spectral centroid estimate is discussed.
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| 10. |
- Tao, Xiao-Jiao, et al.
(author)
-
Narrowband acoustic doppler volume backscattering signal-part II : spectral centroid estimation
- 2002
-
In: IEEE Transactions on Signal Processing. - : IEEE. - 1053-587X .- 1941-0476. ; 50:10, s. 2656-2660
-
Journal article (peer-reviewed)abstract
- This paper proposes a novel algorithm to estimate the time-varying spectral centroid of the narrowband Doppler volume backscattering signal. It is constructed in a semi-parametric way, that is, modeling parametrically the local narrowband evolutionary spectrum using an AR(2) and nonparametrically adapting its time-varying coefficients using the wavelet shrinkage. The improved performance is gained by the underlying linear prediction function of the AR(2) and the minimax optimality of the unknown smoothness adaptation of the wavelet shrinkage procedure.
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