Third-codon transversion rate-based _Nymphaea_ basal angiosperm phylogeny -- concordance with developmental evidence

Flowering plants (angiosperms) appeared on Earth rather suddenly approximately 130 million years ago and underwent a massive expansion in the subsequent 10-12 million years. Current molecular phylogenies have predominantly identified _Amborella_, followed by _Nymphaea_ (water lilies) or _Amborella_ plus _Nymphaea_, in the ANITA clade (_Amborella_, Nymphaeales, Illiciaceae, Trimeniaceae and Austrobaileyaceae) as the earliest angiosperm. However, developmental studies suggest that the earliest angiosperm had a 4-cell/4-nucleus female gametophyte and a diploid endosperm represented by _Nymphaea_, suggesting that _Amborella_, having an 8-cell/9-nucleus female gametophyte and a triploid endosperm, cannot be representative of the basal angiosperm. This evolution-development discordance is possibly caused by erroneous inference based on phylogenetic signals with low neutrality and/or high saturation. Here we show that the 3rd codon transversion (P3Tv), with high neutrality and low saturation, is a robust high-resolution phylogenetic signal for such divergences and that the P3Tv-based land plant phylogeny cautiously identifies _Nymphaea_, followed by _Amborella_, as the most basal among the angiosperm species examined in this study. This P3Tv-based phylogeny contributes insights to the origin of angiosperms with concordance to fossil and stomata development evidence

Two Optimization Ways of DDR3 Transmission Line Equal-Length Wiring Based on Signal Integrity

As we enter the 5G (5th-Generation) era, the amount of information and data has become increasingly tremendous. Therefore, electronic circuits need to have higher chip density, faster operating speed and better signal quality of transmission. As the carrier of electronic components, the design difficulty of high-speed PCB (Printed Circuit Board) is also increasing. Equal-length wiring is an essential part of PCB design. But now, it can no longer meet the needs of designers. Accordingly, in view of the shortcomings of the traditional equal-length wiring, this article proposes two optimization ways: the "spiral wiring" way and the "double spiral wiring" way. Based on the theoretical analysis of the transmission lines, the two optimization ways take the three aspects of optimizing the layout and wiring space, suppressing crosstalk and reducing reflection as the main points to optimize the design. Eventually, this article performs simulation and verification of schematic diagram and PCB of the optimal design by using HyperLynx simulation software. The simulation results show that these two ways not only improve the flexibility of the transmission line layout, but also improve the signal integrity of the transmission lines. Of course, this also proves the feasibility and reliability of the two optimized designs

An Enhanced IEEE1588 Clock Synchronization for Link Delays Based on a System-on-Chip Platform

The clock synchronization is considered as a key technology in the time-sensitive networking (TSN) of 5G fronthaul. This paper proposes a clock synchronization enhancement method to optimize the link delays, in order to improve synchronization accuracy. First, all the synchronization dates are filtered twice to get the good calculation results in the processor, and then FPGA adjust the timer on the slave side to complete clock synchronization. This method is implemented by Xilinx Zynq UltraScale+ MPSoC (multiprocessor system-on-chip), using FPGA+ARM software and hardware co-design platform. The master and slave output Pulse Per-Second (PPS) signals. The synchronization accuracy was evaluated by measuring the time offset between PPS signals. Contraposing the TSN, this paper compares the performance of the proposed scheme with some previous methods to show the efficacy of the proposed work. The results show that the slave clock of proposed method is synchronized with the master clock, leading to better robustness and significant improvement in accuracy, with time offset within the range of 40 nanoseconds. This method can be applied to the time synchronization of the 5G open fronthaul network and meets some special service needs in 5G communication

MicroSyn: A user friendly tool for detection of microsynteny in a gene family

<p>Abstract</p> <p>Background</p> <p>The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes.</p> <p>Results</p> <p>We introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to determine the relationship between two members in a gene family. The colinearity of homologous pairs is controlled by a statistical distance function. As a result, gene duplication history can be inferred from the output independent of gene sequences. MicroSyn was designed for both experienced and non-expert users with a user-friendly graphical-user interface. MicroSyn is available from: <url>http://fcsb.njau.edu.cn/microsyn/</url>.</p> <p>Conclusions</p> <p>Case studies of the microRNA167 genes in plants and Xyloglucan ndotransglycosylase/Hydrolase family in <it>Populus trichocarpa </it>were presented to show the utility of the software. The easy using of MicroSyn in these examples suggests that the software is an additional valuable means to address the problem intrinsic in the computational methods and sequence qualities themselves in gene family analysis.</p

Small Leaks Sink a Great Ship: An Evaluation of Key Reuse Resilience of PQC Third Round Finalist NTRU-HRSS

NTRU is regarded as an appealing finalist due to its long history against all known attacks and relatively high efficiency. In the third round of the NIST competition, the submitted NTRU cryptosystem is the merger of NTRU-HPS and NTRU-HRSS. In 2019, Ding et al. have analyzed the case when the public key is reused for the original NTRU scheme. However, NTRU-HRSS selects coefficients in an arbitrary way, instead of fixed-weight sample spaces in the original NTRU and NTRU-HPS. Therefore, their method cannot be applied to NTRU-HRSS. To address this problem, we propose a full key mismatch attack on NTRU-HRSS. Firstly, we find a longest chain which helps us in recovering the following coefficients. Next, the most influential interference factors are eliminated by increasing the weight of targeted coefficients. In this step, we adaptively select the weights according to the feedbacks of the oracle to avoid errors. Finally, experiments show that we succeed in recovering all coefficients of the secret key in NTRU-HRSS with a success rate of $93.6\%$. Furthermore, we illustrate the trade-off among the success rate, average number of queries, and average time. Particularly, we show that when the success rate is 93.6\%, it has the minimum number of queries at the same time

Mini-PointNetPlus: a local feature descriptor in deep learning model for 3d environment perception

Common deep learning models for 3D environment perception often use pillarization/voxelization methods to convert point cloud data into pillars/voxels and then process it with a 2D/3D convolutional neural network (CNN). The pioneer work PointNet has been widely applied as a local feature descriptor, a fundamental component in deep learning models for 3D perception, to extract features of a point cloud. This is achieved by using a symmetric max-pooling operator which provides unique pillar/voxel features. However, by ignoring most of the points, the max-pooling operator causes an information loss, which reduces the model performance. To address this issue, we propose a novel local feature descriptor, mini-PointNetPlus, as an alternative for plug-and-play to PointNet. Our basic idea is to separately project the data points to the individual features considered, each leading to a permutation invariant. Thus, the proposed descriptor transforms an unordered point cloud to a stable order. The vanilla PointNet is proved to be a special case of our mini-PointNetPlus. Due to fully utilizing the features by the proposed descriptor, we demonstrate in experiment a considerable performance improvement for 3D perception

Over expression of Zmda1-1 gene increases seed mass of corn

Genetic engineering of seed size and increasing biomass in crop plants has an important significant contribution to the world. Arabidopsis DA1 is one of the key factors that negatively control seed and organ size by restricting the period of cell proliferation, and the mutant of Arabidopsis DA1, da1-1 (DA1R358K) can dramatically increase the size of seed. However, it is not clear whether overexpression of Zmda1-1, the mutant of ZmDA1 which is homology of DA1 in Arabidopsis, has the same biological effect as da1-1 in Arabidopsis. Therefore, in this study, the plant expression vector harboring both Zmda1-1 driven by the corn ubiquitin promoter and a PAT selectable marker gene driven by 35S CAMV promoter was constructed and introduced into maize inbred line ‘ji444’ using pollen-tube-pathway method. Screened with herbicide phosphinothricin (PPT), 22 seedlings of 2563 transformed samples survived, and 21 independence lines of which were positive in polymerase chain reaction (PCR) analysis, and the transformation rate of T0 generation was about 0.82%. Further PCR-southern blotting results proved that the Zmda1-1 had integrated into maize genome, and the Zmda1-1 had expression in low level by reverse transcription-polymerase chain reaction (RT-PCR) analysis. The seed mass of transgenic maize increased at an average of 33.6% of empty vector control lines, and the harvest yield was increased by 23.6 to 114.1% in different lines than empty vector control lines. The result suggests that Zmda1-1 can be used to engineer higher harvest yield in crops plant, thus providing the first successful example of increasing the harvest yield of maize by transgenic technology.Key words: Transgenic maize, pollen-tube pathway, Zmda1-1, seed mass

Find the Bad Apples: An efficient method for perfect key recovery under imperfect SCA oracles – A case study of Kyber

Side-channel resilience is a crucial feature when assessing whether a postquantum cryptographic proposal is sufficiently mature to be deployed. In this paper, we propose a generic and efficient adaptive approach to improve the sample complexity (i.e., the required number of traces) of plaintext-checking (PC) oracle-based sidechannel attacks (SCAs), a major class of key recovery chosen-ciphertext SCAs on lattice-based key encapsulation mechanisms (KEMs). This new approach is preferable when the constructed PC oracle is imperfect, which is common in practice, and its basic idea is to design new detection codes that can determine erroneous positions in the initially recovered secret key. These secret entries are further corrected with a small number of additional traces. This work benefits from the generality of PC oracle and thus is applicable to various schemes and implementations. Our main target is Kyber since it has been selected by NIST as the KEM algorithm for standardization. We instantiated the proposed generic attack on Kyber512 and then conducted extensive computer simulations against Kyber512 and FireSaber. We further mounted an electromagnetic (EM) attack against an optimized implementation of Kyber512 in the pqm4 library running on an STM32F407G board with an ARM Cortex-M4 microcontroller. These simulations and real-world experiments demonstrate that the newly proposed attack could greatly improve the state-of-the-art in terms of the required number of traces. For instance, the new attack requires only 41% of the EM traces needed in a majority-voting attack in our experiments, where the raw oracle accuracy is fixed