Regulation and evolution of alternative splicing in plants

Recent studies showed that alternative splicing (AS) is much more prevalent in plants than previously thought. Both genome-wide analyses and cases studies of AS in response to abiotic stresses indicate the importance of AS for plant adaptation in a changing environment. However, how plants regulate their AS in response to herbivore attack, one of major biotic stresses that threaten plant fitness, remains unknown. The tight association between AS and environmental stresses also points to the rapid evolution of AS. However, the underlying mechanisms for this rapid evolution are unknown in plants. In this thesis, I aimed to address these two main questions by investigating the genome-wide insect herbivore-induced AS alteration in wild tobacco (Nicotiana attenuata) and by systematically studying the mechanisms that contributed to the evolution of AS among six plant species

Integral Control on Lie Groups

In this paper, we extend the popular integral control technique to systems evolving on Lie groups. More explicitly, we provide an alternative definition of "integral action" for proportional(-derivative)-controlled systems whose configuration evolves on a nonlinear space, where configuration errors cannot be simply added up to compute a definite integral. We then prove that the proposed integral control allows to cancel the drift induced by a constant bias in both first order (velocity) and second order (torque) control inputs for fully actuated systems evolving on abstract Lie groups. We illustrate the approach by 3-dimensional motion control applications.Comment: Resubmitted to Systems and Control Letters, February 201

Geometric interpretation for A-fidelity and its relation with Bures fidelity

A geometric interpretation for the A-fidelity between two states of a qubit system is presented, which leads to an upper bound of the Bures fidelity. The metrics defined based on the A-fidelity are studied by numerical method. An alternative generalization of the A-fidelity, which has the same geometric picture, to a $N$-state quantum system is also discussed.Comment: 4 pages, 1 figure. Phys. Rev.

Synchronization of kuramoto oscillators with non-identical natural frequencies: a quantum dynamical decoupling approach

This paper proposes a method to counter the drift associated to unknown non-identical natural frequencies in the Kuramoto model of coupled oscillators. Inspired by the quantum dynamical decoupling technique, it builds on a time-varying variant of the dynamics to effectively bring the oscillator phases closer to the same value. This allows effective synchronization despite arbitrarily large differences in natural frequencies. For two agents admitting instantaneous position exchanges, we exactly compute how the relative phase converges to a stable periodic fixed point. The latter tends to zero when the dynamics switches at a faster rate. With continuous state evolutions, using a related dynamic controller instead of instantaneous jumps, we show with a Lyapunov function that exact phase synchronization is obtained. We generalize the method to multiple oscillators with instantaneous state exchanges, that can be implemented by cycling through a predefined or random sequence of exchanges. Simulation results illustrate the effectiveness of the algorithms

WaveAttack: Asymmetric Frequency Obfuscation-based Backdoor Attacks Against Deep Neural Networks

Due to the popularity of Artificial Intelligence (AI) technology, numerous backdoor attacks are designed by adversaries to mislead deep neural network predictions by manipulating training samples and training processes. Although backdoor attacks are effective in various real scenarios, they still suffer from the problems of both low fidelity of poisoned samples and non-negligible transfer in latent space, which make them easily detectable by existing backdoor detection algorithms. To overcome the weakness, this paper proposes a novel frequency-based backdoor attack method named WaveAttack, which obtains image high-frequency features through Discrete Wavelet Transform (DWT) to generate backdoor triggers. Furthermore, we introduce an asymmetric frequency obfuscation method, which can add an adaptive residual in the training and inference stage to improve the impact of triggers and further enhance the effectiveness of WaveAttack. Comprehensive experimental results show that WaveAttack not only achieves higher stealthiness and effectiveness, but also outperforms state-of-the-art (SOTA) backdoor attack methods in the fidelity of images by up to 28.27\% improvement in PSNR, 1.61\% improvement in SSIM, and 70.59\% reduction in IS

Bounds of concurrence and their relation with fidelity and frontier states

The bounds of concurrence in [F. Mintert and A. Buchleitner, Phys. Rev. Lett. 98 (2007) 140505] and [C. Zhang \textit{et. al.}, Phys. Rev. A 78 (2008) 042308] are proved by using two properties of the fidelity. In two-qubit systems, for a given value of concurrence, the states achieving the maximal upper bound, the minimal lower bound or the maximal difference upper-lower bound are determined analytically

Development of Omni InDel and supporting database for maize

Insertions–deletions (InDels) are the second most abundant molecular marker in the genome and have been widely used in molecular biology research along with simple sequence repeats (SSR) and single-nucleotide polymorphisms (SNP). However, InDel variant mining and marker development usually focuses on a single type of dimorphic InDel, which does not reflect the overall InDel diversity across the genome. Here, we developed Omni InDels for maize, soybean, and rice based on sequencing data and genome assembly that included InDel variants with base lengths from 1 bp to several Mb, and we conducted a detailed classification of Omni InDels. Moreover, we screened a set of InDels that are easily detected and typed (Perfect InDels) from the Omni InDels, verified the site authenticity using 3,587 germplasm resources from 11 groups, and analyzed the germplasm resources. Furthermore, we developed a Multi-InDel set based on the Omni InDels; each Multi-InDel contains multiple InDels, which greatly increases site polymorphism, they can be detected in multiple platforms such as fluorescent capillary electrophoresis and sequencing. Finally, we developed an online database website to make Omni InDels easy to use and share and developed a visual browsing function called “Variant viewer” for all Omni InDel sites to better display the variant distribution

Nicotiana attenuata Data Hub (NaDH): an integrative platform for exploring genomic, transcriptomic and metabolomic data in wild tobacco

Background: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now. Description: We present the Nicotiana attenuata Data Hub (NaDH) as a centralized platform for integrating and visualizing genomic, phylogenomic, transcriptomic and metabolomic data in N. attenuata. The NaDH currently hosts collections of predicted protein coding sequences of 11 plant species, including two recently sequenced Nicotiana species, and their functional annotations, 222 microarray datasets from 10 different experiments, a transcriptomic atlas based on 20 RNA-seq expression profiles and a metabolomic atlas based on 895 metabolite spectra analyzed by mass spectrometry. We implemented several visualization tools, including a modified version of the Electronic Fluorescent Pictograph (eFP) browser, co-expression networks and the Interactive Tree Of Life (iTOL) for studying gene expression divergence among duplicated homologous. In addition, the NaDH allows researchers to query phylogenetic trees of 16,305 gene families and provides tools for analyzing their evolutionary history. Furthermore, we also implemented tools to identify co-expressed genes and metabolites, which can be used for predicting the functions of genes. Using the transcription factor NaMYB8 as an example, we illustrate that the tools and data in NaDH can facilitate identification of candidate genes involved in the biosynthesis of specialized metabolites. Conclusion: The NaDH provides interactive visualization and data analysis tools that integrate the expression and evolutionary history of genes in Nicotiana, which can facilitate rapid gene discovery and comparative genomic analysis. Because N. attenuata shares many genome-wide features with other Nicotiana species including cultivated tobacco, and hence NaDH can be a resource for exploring the function and evolution of genes in Nicotiana species in general. The NaDH can be accessed at: http://nadh.ice.mpg.de

Fidelity induced distance measures for quantum states

Fidelity plays an important role in quantum information theory. In this letter, we introduce new metric of quantum states induced by fidelity, and connect it with the well-known trace metric, Sine metric and Bures metric for the qubit case. The metric character is also presented for the qudit (i.e., $d$-dimensional system) case. The CPT contractive property and joint convex property of the metric are also studied.Comment: 8 page