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With the rapid development of machine learning technologies in recent years, different types of neural network (NN)-based equalizers have been proposed and proved to be efficient digital signal processing tools to deal with the nonlinear impairments in short-reach direct detection optical interconnects. However, one major concern for these NN-based equalizers is their computational complexity (CC), since only a few tens of multiplications per symbol can be practically handled considering real-time implementation. In this paper, we propose an NN-based multi-symbol equalization scheme inspired by multi-task learning. Compared with traditional single-output NN-based equalizers, the CC can be significantly reduced with the help of the proposed scheme. A 50-Gb/s 25-km pulse amplitude modulation (PAM)-4 direct detection optical link is experimentally carried out and 3 different types of NNs, i.e., feedforward NN (FNN), cascade FNN (C-FNN), and recurrent NN (RNN), are employed for the proposed multi-symbol equalization scheme. Experimental results show that a maximum CC reduction of 43.2%/41.1%/44.0% can be achieved with FNN/C-FNN/RNN-based multi-symbol equalization to achieve their best performance, compared with the corresponding single-output NNs. The best performance of the proposed and the traditional FNN/-C-FNN-based schemes are the same, while the RNN-based scheme sacrifices a slight system performance. Aided by multi-symbol equalization, the CC needed to recover 1 symbol for various NNs can all be reduced to about a few tens of multiplications, indicating the feasibility of real-time implementation of these NN-based equalizers.

Coherent detection has the primary advantage of optical field recovery, which enables channel impairment compensation and advanced modulation formats for high-capacity transmission. On the other hand, direct detection (DD) is more cost-effective due to its local oscillator (LO)-free detection. To gain the field recovery advantage while preserving the LO-free detection for DD-based receivers, carrier assisted differential detection (CADD) has been proposed to retrieve the complex-valued double-sideband (DSB) signal. In this paper, to extend the concept of CADD, we propose a simplified CADD scheme with reduced hardware complexity and present signal-to-signal beating interference (SSBI) iterative mitigation algorithms with and without symbol decision. The required number of photodetectors and analog-digital converters (ADCs) for the simplified CADD receiver becomes the same as the coherent homodyne counterpart but without needing the expensive narrow-linewidth LOs. The performance of the proposed simplified CADD receiver is evaluated by 60-Gbaud 16-QAM DSB signals. Extensive performance comparisons are made between (i) the generalized CADD receivers with and without the simplified receiver structure, (ii) SSBI iterative mitigation algorithm with and without the symbol decision, and (iii) single carrier (SC) and OFDM-modulated DSB signals for the simplified CADD receiver.

DNA methylation is changed and associates with gene expression alterations in plant response to phosphate starvation (Pi-), a common stress that impacts plant growth and productivity. However, in the horticultural model species Solanum lycopersicum (tomato), the dynamics of DNA methylation and its relationship with changes in gene transcription and alternative splicing (AS) under Pi- are unknown. Here, we performed integrative methylome and transcriptome analyses of tomato seedlings under Pi-deficient and -sufficient conditions. We found Pi- caused a slight increase in the overall methylation level, with millions of differentially methylated cytosines (DmCs) and a few hundred differentially methylated regions (DMRs). We also identified thousands of differentially expressed (DE) and differential AS (DAS) genes induced by Pi-, and found that DmCs were more abundant in non-expressed genes than in DE or DAS genes. Moreover, DNA methylation alterations weakly correlated with transcription changes but not with DAS events, and hyper-CHH-DMRs overlapping with transposable elements (TEs) were enriched in a subset of Pi starvation response (PSR) genes. We propose that changes in DNA methylation may be associated with the differential expression of some PSR genes, but that most of these changes probably control the expression of nearby TEs, rather than directly affecting the transcription or AS of PSR genes. Besides, the pattern of methylation changes upon Pi- may largely be shaped by TE distributions. Together, our study provides comprehensive insights into the association of DNA methylation with gene transcription and AS under Pi- in tomato and may contribute to unveiling novel roles of epigenetic mechanisms in plant stress response.

Conventional supervised binary classification algorithms have been widely applied to address significant research questions using biological and biomedical data. This classification scheme requires two fully labeled classes of data (e.g. positive and negative samples) to train a classification model. However, in many bioinformatics applications, labeling data is laborious, and the negative samples might be potentially mislabeled due to the limited sensitivity of the experimental equipment. The positive unlabeled (PU) learning scheme was therefore proposed to enable the classifier to learn directly from limited positive samples and a large number of unlabeled samples (i.e. a mixture of positive or negative samples). To date, several PU learning algorithms have been developed to address various biological questions, such as sequence identification, functional site characterization and interaction prediction. In this paper, we revisit a collection of 29 state-of-the-art PU learning bioinformatic applications to address various biological questions. Various important aspects are extensively discussed, including PU learning methodology, biological application, classifier design and evaluation strategy. We also comment on the existing issues of PU learning and offer our perspectives for the future development of PU learning applications. We anticipate that our work serves as an instrumental guideline for a better understanding of the PU learning framework in bioinformatics and further developing next-generation PU learning frameworks for critical biological applications.

We propose NN-based multi-symbol equalization for a 50-Gb/s PAM4 direct-detection link which significantly reduces computational complexity without sacrificing BER performance of conventional single-output NNs. Complexity reduction of 42.7% is achieved when 8 outputs are selected.

A simplified short-blocklength variable-to-fixed distribution matching algorithm is proposed for probabilistic shaping. Compared with the original V2F DMLP method, the computational cost is reduced to 0.41 operations per bit, which is 15 times less.

Class III peroxidases (CIII Prxs) play critical roles in plant immunity by scavenging reactive oxygen species (ROS). However, the functions of CIII Prxs in rice (Oryza sativa L.) immunity are largely unexplored. Here, we report a Prx precursor, OsPrx30, that is responsive to the bacterial blight Xanthomonas oryzae pv. oryzae (Xoo). OsPrx30 was primarily expressed in rice roots, leaves, and stems, and its protein product was mainly localized at the endoplasmic reticulum. Overexpression of OsPrx30 enhanced the plant's susceptibility to Xoo by maintaining a high level of peroxidase (POD) activity and reducing the content of H2 O2 , whereas depletion of OsPrx30 had the opposite effects. Furthermore, we identified an AT-hook transcription factor, OsATH1, that is specifically bound to the OsPrx30 promoter. As observed in plants overexpressing OsPrx30, depletion of OsATH1 enhanced susceptibility to Xoo. Finally, we demonstrated that depletion of OsATH1 increased histone H3 acetylation at the AT-rich region of the OsPrx30 promoter. Taken together, these results reveal a mechanism underlying the POD-induced natural resistance to bacterial diseases and suggest a model for transcription regulation of Prx genes in rice.

This paper presents a global dynamic surface control (DSC) method for a class of uncertain multi-input/multi-output (MIMO) pure-feedback nonlinear systems with non-affine functions possibly being in-differentiable. It is well known that the traditional DSC method is commonly used for reducing the design complexity of the backstepping control method; however, the regulation results of the DSC method are semi-global uniformly ultimately bounded (SGUUB). An improved DSC (IDSC) method is first designed in this paper so that the results are global uniformly ultimately bounded (GUUB). Comparing with the traditional DSC method, the parameters of first-order filters in IDSC are time varying rather than constants. The control design for MIMO pure-feedback nonlinear systems researched is much more complex than the SISO cases, and the presence of in-differentiable non-affine functions considered in this paper makes the control design even more difficult. Therefore, we proposed the IDSC method, which can significantly reduce the complexity of the control design for the MIMO pure-feedback nonlinear systems in cooperation with the backstepping method, and it is proved that IDSC can guarantee the GUUB of all the signals of the system. Finally, the simulation results are provided to demonstrate the effectiveness of the designed method.

MicroRNAs (miRNAs) play an important role in plant growth, development and responses to stresses. Rice blast is one of the most devastating diseases in rice production. However, little is known regarding the effects of miRNAs response to rice blast. Herein, by deep sequencing small RNA from the susceptible line ZhongerRuanzhan and its space-induced blast resistant mutant line H4 under normal conditions and upon Magnaporthe oryzae (M. orzyzae) infection, several known miRNAs were detected and their expression profiles were found to be negatively correlated with their targets. And, a total of 50 novel miRNAs induced by M. oryzae infection were also identified from four small RNA libraries. Moreover, 176 putative targets of 23 novel miRNAs, which are involved in the various functions, were validated by two degradome analysis. Six novel miRNAs were selected for further validation with qRT-PCR analysis and the results showed that their expression levels were associated with blast response. The knowledge obtained in this study will help us understanding the functions of miRNAs and their targets in regulating blast resistance.

Flowering or heading is one of most important agronomic traits in rice. It has been characterized that CONSTANS (CO) and CONSTANS-like (COL) proteins are critical flowering regulators in response to photoperiodic stress in plants. We have previously identified that the COL family member OsCOL9 can positively enhance the rice blast resistance. In the present study, we aimed to explore the functional role of OsCOL9 in modulating the photoperiodic flowering. Our data showed that overexpression of OsCOL9 delayed the flowering time under both short-day (SD) and long-day (LD) conditions, leading to suppressed expressions of EHd1, RFT and Hd3a at the mRNA Level. OsCOL9 expression exhibited two types of circadian patterns under different daylight conditions, and it could delay the heading date by suppressing the Ehd1 photoperiodic flowering pathway. In contrast, the expressions of previously reported flowering regulators were not significantly changed in OsCOL9 transgenic plants, indicating that OsCOL9 functioned independently of other flowering pathways. In addition, OsCOL9 served as a potential yield gene, and its deficiency reduced the grain number of main panicle in plants. Furthermore, yeast two-hybrid assay indicated that OsCOL9 physically interacted with Receptor for Activated C-kinase 1 (OsRACK1). Rhythmic pattern analysis suggested that OsRACK1 responded to the change of daylight, which was regulated by the circadian clock. Taken together, our results revealed that OsCOL9 could delay the flowering time in rice by repressing the Ehd1 pathway.

A novel scheme for disturbance observer is designed for an extended class of strict-feedback nonlinear systems with possibly unbounded, non-smooth, and state-independent compounded disturbance. To overcome these problems in disturbance observer design, the typical slide mode differentiators are improved by introducing hyperbolic tangent function to make the signals smooth, and then the improved slide mode differentiators are constructively used to estimate the errors of variables in the presence of disturbances. The unbounded, non-smooth or state-independent disturbances are therefore able to be eliminated by using the estimated variable errors. Thus, the bounded or differentiable conditions for disturbance observer design are removed. Furthermore, the convergence of the new disturbance observer is rigorously proved based on Lyapunov stability theorem, and the tracking error can be arbitrarily small. Finally, the simulation results are given to validate the feasibility and superiority of the proposed approach.

The regulation of innate immunity and plant growth, along with the trade-off between them, affects the defense and recovery mechanisms of the plant after it is attacked by pathogens. Although it is known that hormonal crosstalk plays a major role in regulating interaction of plant growth and PAMP-triggered immunity, the relationship between plant growth and effector-triggered immunity (ETI) remains unclear. In a large-scale yeast two-hybrid screening for Pik-H4-interacting proteins, a homeodomain transcription factor OsBIHD1 was identified, which is previously known to function in biotic and abiotic stress responses. The knockout of OsBIHD1 in rice lines carrying Pik-H4 largely compromised the resistance of the rice lines to Magnaporthe oryzae, the fungus that causes rice blast. While overexpression of OsBIHD1 resulted in enhanced expression of the pathogenesis-related (PR) and ethylene (ET) synthesis genes. Moreover, OsBIHD1 was also found to directly bind to the promoter region of ethylene-synthesis enzyme OsACO3. In addition, OsBIHD1 overexpression or deficiency provoked dwarfism and reduced brassinosteroid (BR) insensitivity through repressing the expression of several critical genes involved in BR biosynthesis and BR signaling. During M. oryzae infection, transcript levels of the crucial BR catabolic genes (CYP734A2, CYP734A4, and CYP734A6) were significantly up-regulated in OsBIHD1-OX plants. Furthermore, OsBIHD1 was found to be capable of binding to the sequence-specific cis-elements on the promoters of CYP734A2 to suppress the plant growth under fungal invasion. Our results collectively suggest a model that OsBIHD1 is required for Pik-H4-mediated blast resistance through modulating the trade-off between resistance and growth by coordinating brassinosteroid-ethylene pathway.

Although adenosine monophosphate (AMP) binding domain is widely distributed in multiple plant species, detailed molecular functions of AMP binding proteins (AMPBPs) in plant development and plant-pathogen interaction remain unclear. In the present study, we identified an AMPBP OsAAE3 from a previous analysis of early responsive genes in rice during Magnaporthe oryzae infection. OsAAE3 is a homologue of Arabidopsis AAE3 in rice, which encodes a 4-coumarate-Co-A ligase (4CL) like protein. A phylogenetic analysis showed that OsAAE3 was most likely 4CL-like 10 in an independent group. OsAAE3 was localized to cytoplasm, and it could be expressed in various tissues. Histochemical staining of transgenic plants carrying OsAAE3 promoter-driven GUS (β-glucuronidase) reporter gene suggested that OsAAE3 was expressed in all tissues of rice. Furthermore, OsAAE3-OX plants showed increased susceptibility to M. Oryzae, and this finding was attributable to decreased expression of pathogen-related 1a (PR1) and low level of peroxidase (POD) activity. Moreover, OsAAE3 over-expression resulted in increased content of H2O2, leading to programmed cell-death induced by reactive oxygen species (ROS). In addition, OsAAE3 over-expression repressed the floret development, exhibiting dramatically twisted glume and decreased fertility rate of anther. Meanwhile, the expressions of lignin biosynthesis genes were significantly decreased in OsAAE3-OX plants, thereby leading to reduced lignin content. Taken together, OsAAE3 functioned as a negative regulator in rice blast resistance, floret development and lignin biosynthesis. Our findings further expanded the knowledge in functions of AMBPs in plant floret development and the regulation of rice-fungus interaction.

Although adenosine monophosphate (AMP) binding domain is widely distributed in multiple plant species, detailed molecular functions of AMP binding proteins (AMPBPs) in plant development and plant-pathogen interaction remain unclear. In the present study, we identified an AMPBP OsAAE3 from a previous analysis of early responsive genes in rice during Magnaporthe oryzae infection. OsAAE3 is a homolog of Arabidopsis AAE3 in rice, which encodes a 4-coumarate-Co-A ligase (4CL) like protein. A phylogenetic analysis showed that OsAAE3 was most likely 4CL-like 10 in an independent group. OsAAE3 was localized to cytoplasm, and it could be expressed in various tissues. Histochemical staining of transgenic plants carrying OsAAE3 promoter-driven GUS (β-glucuronidase) reporter gene suggested that OsAAE3 was expressed in all tissues of rice. Furthermore, OsAAE3-OX plants showed increased susceptibility to M. Oryzae, and this finding was attributable to decreased expression of pathogen-related 1a (PR1) and low level of peroxidase (POD) activity. Moreover, OsAAE3 over-expression resulted in increased content of H2O2, leading to programmed cell-death induced by reactive oxygen species (ROS). In addition, OsAAE3 over-expression repressed the floret development, exhibiting dramatically twisted glume and decreased fertility rate of anther. Meanwhile, the expressions of lignin biosynthesis genes were significantly decreased in OsAAE3-OX plants, thereby leading to reduced lignin content. Taken together, OsAAE3 functioned as a negative regulator in rice blast resistance, floret development, and lignin biosynthesis. Our findings further expanded the knowledge in functions of AMBPs in plant floret development and the regulation of rice-fungus interaction.

Different additional connections onto feedforward neural networks are investigated for equalization in a 50-Gb/s PAM4 short-reach direct detection link. The auto-regressive and cascade structures demonstrate the most significant performance improvement with limited additional computational complexity. © 2020 The Author(s)