Kernel Development Research Articles

Design and Performance Analysis of Short Time Fourier Transform Processor

Abstract: Time-frequency domain characterization of signals have always been focused on variants of Short time Fourier transform (STFT). The selection of transform kernel plays an important role in preserving the signal support which provides a cross-term free time-frequency distribution. Time-Bandwidth product has been taken as a measure of signal support preservation criteria thereby developing an optimal kernel for STFT based on linear canonical decomposition. In the development of kernel , Fractional Fourier Transform (FrFT) is used which provides noise free frequency domain representation .With the help of developed transform kernel , the magnitude-wise shift invariance property is verified and timefrequency content is analyzed by plotting spectrogram. Keywords: STFT, FrFT, kernel, Time-Bandwidth product, spectrogram.

Transcriptome analysis reveals genes associated with kernel size in apricots cultivated for kernel consumption (Prunus armeniaca × Prunus sibirica)

Seed size is an important component of overall seed yield trait, and apricots cultivated for consumable kernels produce kernels that are large and sweet. However, the molecular mechanism of kernel development in kernel consumption apricots remains unclear. We measured kernel weight, length, width, and thickness and investigated the transcriptome profiles of kernel consumption apricots (Prunus armeniaca × Prunus sibirica) at six different developmental stages. The phenotypic analysis results showed that rapid kernel size development occurred from 15 to 45 days after flowering (DAF), and that the kernel coat size almost reached its the maximum at 45 DAF, suggesting that the early kernel development was important factor that determine overall kernel size. A total of 8,108 differentially expressed genes (DEGs) were identified, and a weighted gene co-expression network analysis revealed that turquoise module was strongly correlated with the kernel size. Six hub genes were identified as potential regulators of the kernel size. Furthermore, we analyzed the DEGs related to kernel size in the phytohormones metabolic pathways, ubiquitin-proteasome pathway, G-protein signaling, mitogen-activated protein kinase signaling, and HAIKU pathway, which were considered to be important regulators of kernel size. Our findings provide new insights into the molecular mechanisms underlying the regulation of kernel size in kernel consumption apricots.

2‐D Analytical P‐to‐S and S‐to‐P Scattered Wave Finite Frequency Kernels

AbstractScattered wave imaging provides a powerful tool for understanding Earth's structure. The development of finite frequency kernels for scattered waves has the potential for improving the resolution of both the structure and magnitude of discontinuities in S‐wave velocity. Here we present a 2‐D analytical expression for teleseismic P‐to‐S and S‐to‐P scattered wave finite‐frequency kernels for a homogeneous medium. We verify the accuracy of the kernels by comparing to a spectral element method kernel calculated using SPECFEM2D. Finally, we demonstrate the ability of the kernels to recover seismic velocity discontinuities with a variety of shapes including a flat discontinuity, a discontinuity with a sharp step, a discontinuity with a smooth bump, and an undulating discontinuity. We compare the recovery using the kernel approach to expected recovery assuming the classical common conversion point (CCP) stacking approach. We find that the P‐to‐S kernel increases recovery of all discontinuity structures in comparison to CCP stacking especially for the shallowest discontinuity in the model. The S‐to‐P kernel is less successful but can be useful for recovering the curvature of shallow discontinuity undulations. Finally, although we observe some variability in the amplitude of the kernels along the discontinuities, the kernels show some potential for recovering the magnitude of the velocity contrast across a discontinuity.

Impact of kernel development on phenolic profiles and antioxidant activity in Castanea henryi

SummaryThe changes in the phenolic profiles during the kernel development of two varieties of Castanea henryi (‘Jinzhui’ (YS) and ‘Baiyan No.1’ (WS)) were investigated based on content levels and gene expression levels. The results showed that the total phenolic content (TPC) increased during the Castanea henryi development and were mainly dependent on the content variation of gallic acid and (‐)‐epicatechin. Gene C4H positively affected the accumulation of p‐coumaric acid, while gene CHI and F3H positively affected the biosynthesis of (‐)‐epicatechin. Four assays including DPPH, FRAP, ABTS and ORAC were conducted to evaluate the antioxidant quality of Castanea henryi extracts. The results showed that the Castanea henryi developed at S4 (stage 4) possessed the better antioxidant quality. In addition, in both varieties, FRAP and ORAC value were more likely to be influenced by the variation of gallic acid and (‐)‐epicatechin concentrations, respectively. The DPPH value in YS was dependent on the syringic acid and the gallic acid content in WS.

Expression analysis of opaque2, crtRB1 and shrunken2 genes during different stages of kernel development in biofortified sweet corn

Sweet corn is a popular food worldwide. Traditional shrunken2 (sh2)-derived sweet corn possesses low lysine (0.150–0.250%), tryptophan (0.030–0.040%) and provitamin-A (proA: 3–4 μg/g). Here transcript profiles of a newly developed 12 sh2-based sweet corn inbreds possessing mutant opaque2 (o2) and β-carotene hydroxylase (crtRB1) genes were analyzed during three stages of kernel development viz., 20-, 24- and 28- days after pollination (DAP). Introgressed inbreds had higher lysine (0.309%), tryptophan (0.077%) and proA (17.28 μg/g). Across stages of kernel development, transcript levels of mutant sh2, o2 and crtRB1 genes were significantly lower than the wild type (sh2+, o2+ and crtRB1+) alleles. Among genes, sh2 had the highest level of transcripts accumulation followed by crtRB1 and o2. While o2 and crtRB1 transcripts attained peaks at 24-DAP, the highest peak for sh2 was recorded at 28-DAP. Strong negative correlation (r = −0.99 to −0.71) was observed between the transcripts and corresponding nutrients. The study provided insight of complex regulation of sh2, o2 and crtRB1 genes during various stages of kernel development. This is a first of its kind study to analyze the transcript level variation of mutant allele of sh2, o2 and crtRB1 genes among novel biofortified sweet corn genotypes.

Genome-Wide Identification, Characterization, and Expression Profiling of AP2/ERF Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (Carya illinoinensis).

The ethylene-responsive element (AP2/ERF) is one of the keys and conserved transcription factors (TFs) in plants that play a vital role in regulating plant growth, development, and stress response. A total of 202 AP2/ERF genes were identified from the pecan genome and renamed according to the chromosomal distribution of the CiAP2/ERF genes. They were divided into four subfamilies according to the domain and phylogenetic analysis, including 26 AP2, 168 ERF, six RAV, and two Soloist gene family members. These genes were distributed randomly across the 16 chromosomes, and we found 19 tandem and 146 segmental duplications which arose from ancient duplication events. The gene structure and conserved motif analysis demonstrated the conserved nature of intron/exon organization and motifs among the AP2/ERF genes. Several cis-regulatory elements, which were related to light responsiveness, stress, and defense responses, were identified in the promoter regions of AP2/ERFs. The expression profiling of 202 CiAP2/ERF genes was assessed by using RNA-Seq data and qRT-PCR during development (pistillate flowering development, graft union development, and kernel development) and under abiotic stresses (waterlogging, drought). Moreover, the results suggested that the ERF-VII members may play a critical role in waterlogging stress. These findings provided new insights into AP2/ERF gene evolution and divergence in pecan and can be considered a valuable resource for further functional validation, as well as for utilization in a stress-resistance-variety development program.

Graph kernels based on optimal node assignment

The success of kernel algorithms depends on the kernel it uses and hence the development of kernels for structured data like graphs is an active research field. We designed two graph kernels by making use of the optimal assignment kernel framework, which is a less explored graph framework compared to its counterpart, namely, R-convolution kernels. In our work, the bijection associated with the optimal assignment framework is defined between sets that consist of the nodes of the graph kernel arguments and hence we named the proposed kernels as optimal node assignment kernels (ONA). In ONA, the nodes of the given data are divided into groups named as neighbourhood sets on the basis of the labels generated by the Weisfeiler–Lehman (WL) test for graph isomorphism and a matrix representation is defined for them. A kernel is then defined over the domain that consists of the neighbourhood sets in terms of such matrices and an aggregate measure of those kernel values is used for defining ONA kernel. The validity of the proposed kernels is mathematically proved. The kernel calculation using the hierarchy structure associated with the optimal assignment framework is also discussed. The performance of the proposed ONA kernels was analysed using graph classification datasets and was found to be superior in comparison with the other state-of-the-art graph kernels.

Genetic analysis and molecular characterization of a novel maize <italic>Bt2 </italic>gene mutant

<p id="C3">The research of the molecular mechanism underlying maize kernel development is particularly important for the genetic improvement of maize yield and quality traits. In this study, we characterized a new shrunken kernel mutant <italic>5601Q</italic>, which was generated by a random transposon insertion. Genetic analysis indicated that the kernel phenotype was stably controlled by a single recessive gene. F₂ segregating population was constructed by crossing <italic>5601Q</italic> into B73 inbred line, and the mutant gene was located in the genetic interval of 60.19-62.58 Mb on chromosome 4. Sequence annotation showed that the <italic>BRITTLE ENDOSPERM2 </italic>(<italic>Bt2</italic>) gene, previously reported to be involved in maize kernel development, was located in this region. Maize<italic> Bt2</italic> gene encoded the small subunit of ADP-glucose pyrophosphorylase (AGPase), the first rate-limiting enzyme in the starch biosynthetic pathway of higher plants. Compared with wild type, 100-grain weight and starch content of mutant <italic>5601Q</italic> decreased significantly, but the soluble sugar content increased dramatically 4.67 times. We confirmed that <italic>5601Q</italic> was a new allele mutant of <italic>Bt2</italic> by allelic test of <italic>Bt2</italic> mutant <italic>1774 </italic>and<italic> 5601Q</italic>. Sequencing analysis revealed that <italic>Mutator 19 </italic>transposon was inserted in the 2nd exon of <italic>Bt2</italic> gene. In summary, our results indicated that the shrunken kernel in <italic>5601Q </italic>was caused by the loss-of-function of <italic>Bt2 </italic>gene, which provided a new germplasm resource to elucidate the mechanism of maize <italic>Bt2 </italic>gene in endosperm storage substance accumulation.

A new network containing MYB109-ZmCesA5 is involved in kernel development

MYB genes regulate several different aspects of metabolism and development. However, few studies have reported the involvement of MYBs-CesAs network in the regulation of maize kernel development. In this study, yeast one-hybrid (Y1H) assays and dual-luciferase reporter assays showed that ZmMYB109 activated the expression of ZmCesA5 by directly binding to its promoter. Real-time quantitative PCR (RT-qPCR) and transcriptome analyses showed that ZmMYB109 expression increased in ZmCesA5-OE kernels and decreased in ZmCesA5-KO kernels. Overexpression of ZmCesA5 produced heavier kernels, whereas loss of function of ZmCesA5 affected starch and sucrose metabolism, resulting in weight reduction of the maize kernels. Collectively, these findings suggest that a new network containing MYB109-ZmCesA5 is involved in kernel development.

Comparative Transcriptome Analysis Reveals Differential Regulation of Flavonoids Biosynthesis Between Kernels of Two Pecan Cultivars.

Flavonoids influence the flavor and nutritional value of pecan nuts. However, limited information is available regarding the molecular mechanisms underlying pecan flavonoid biosynthesis. Here, we used a high (“YLC28”) and a low (“Oconee”) flavonoid content cultivar as the research objects. The changes in flavonoid content and the gene transcription patterns during kernel development were identified. Different accumulation patterns of total flavonoids (TF) and condensed tannins (CT) were observed between the two cultivars. The contents of TF and CT in “YLC28” were 1.76- and 2.67-fold higher levels than that of “Oconee” on 150 days after full bloom of female flowers, respectively. In total, 30 RNA-Seq libraries were constructed and sequenced. The upregulated genes in “YLC28” were highly enriched in flavonoid-related pathways. Thirty-three structural genes were identified, and the expression of two phenylalanine ammonia lyases, one chalcone synthase, one flavonoid 3’,5’-hydroxylase, and one flavonol synthase exhibited high correlation (r ≥ 0.7, p < 0.01) with the condensed tannin content in “YLC28.” A putative MYB transcription factor, CIL1093S0100, might act as a flavonoid biosynthesis repressor during kernel development. Altogether, these results will be useful for uncovering the molecular mechanisms of flavonoid biosynthesis and subsequently accelerating quality pecan breeding.

Tension between predicting accurate ground state correlation energies and excitation energies from adiabatic approximations in TDDFT.

The connection between the adiabatic excitation energy of time-dependent density functional theory and the ground state correlation energy from the adiabatic connection fluctuation-dissipation theorem (ACFDT) is explored in the limiting case of one excited state. An exact expression is derived for any adiabatic Hartree-exchange-correlation kernel that connects the excitation energy and the potential contribution to correlation. The resulting formula is applied to the asymmetric Hubbard dimer, a system where this limit is exact. Results from a hierarchy of approximations to the kernel, including the random phase approximation (RPA) with and without exchange and the adiabatically exact (AE) approximation, are compared to the exact ones. At full coupling, the numerical results indicate a tension between predicting an accurate excitation energy and an accurate potential contribution to correlation. The AE approximation is capable of making accurate predictions of both quantities, but only in parts of the parameter space that classify as weakly correlated, while RPA tends to be unable to accurately predict these properties simultaneously anywhere. For a strongly correlated dimer, the AE approximation greatly overestimates the excitation energy yet continues to yield an accurate ground state correlation energy due to its accurate prediction of the adiabatic connection integrand. If similar trends hold for real systems, the development of correlation kernels will be important for applications of the ACFDT in systems with large potential contributions to correlation.

Modeling of the effects of non-equilibrium excitation and electrode geometry on H2/air ignition in a nanosecond plasma discharge

This work presents the results of two-dimensional modeling of the effects of non-equilibrium excitation and electrode geometry on H2/air ignition in a nanosecond plasma discharge. A multiscale adaptive reduced chemistry solver for plasma assisted combustion (MARCS-PAC) based on PASSKEy discharge modeling package and compressible multi-component reactive flow solver ASURF+ is developed and validated. This model is applied to simulate the impact of non-equilibrium plasma excitation and electrode geometry and heat loss on the dynamics of the discharge from streamer to spark and ignition kernel development in a H2/air mixture with a pair of cylindrical electrodes. The results show that the plasma-generated species (N2(A), N2(B), N2(a′), N2(C), O(1D), O and H) in the spark and afterglow significantly accelerate the ignition kernel development. The increase of discharge voltage at the same total discharge energy promotes the non-equilibrium active species production. It is found that the production of electronically excited species at higher reduced electric field strength is more efficient in enhancing ignition in comparison to the vibrational excitation and heating. Moreover, the 2D simulation clearly reveals that the electric field and active species distribution are highly non-uniform. The streamers are initiated at the sharp outer edges of the negative and positive electrodes by a strong electric field while the electric field is much weaker at the centerline of the electrodes. Furthermore, the simulations reveal that the ignition enhancement is sensitive to the variation of electrode shape, diameter, and gap size due to the changes of electric field distribution and location of streamer formation. A cylindrical electrode produces a larger discharge volume and ignition kernel than the parabolic and spherical electrodes, when the discharge is localized near the axis of the gap. It is found that there is a non-monotonic dependence of ignition kernel size on the electrode diameter and inter-electrode distance. The increase of electrode diameter and gap size above the optimal conditions leads to the reduction of ignition kernel volume, due to the decrease of active species concentration and gas temperature. At a larger electrode surface area and electrode diameter as well as smaller electrode gap size, the heat loss to electrode plays a greater role in reducing the ignition kernel size and slowing ignition kernel development. This work provides insights and guidance to understand the kinetic enhancement of non-equilibrium plasma and the effects of electrode geometries on ignition for the optimization ignitors in advanced engines.

Maize RNA 3'-terminal phosphate cyclase-like protein promotes 18S pre-rRNA cleavage and is important for kernel development.

Plant ribosomes contain four specialized ribonucleic acids, the 5S, 5.8S, 18S, and 25S ribosomal RNAs (rRNAs). Maturation of the latter three rRNAs requires cooperative processing of a single transcript by several endonucleases and exonucleases at specific sites. In maize (Zea mays), the exact nucleases and components required for rRNA processing remain poorly understood. Here, we characterized a conserved RNA 3′-terminal phosphate cyclase (RCL)-like protein, RCL1, that functions in 18S rRNA maturation. RCL1 is highly expressed in the embryo and endosperm during early seed development. Loss of RCL1 function resulted in lethality due to aborted embryo cell differentiation. We also observed pleiotropic defects in the rcl1 endosperm, including abnormal basal transfer cell layer growth and aleurone cell identity, and reduced storage reserve accumulation. The rcl1 seeds had lower levels of mature 18S rRNA and the related precursors were altered in abundance compared with wild type. Analysis of transcript levels and protein accumulation in rcl1 revealed that the observed lower levels of zein and starch synthesis enzymes mainly resulted from effects at the transcriptional and translational levels, respectively. These results demonstrate that RCL1-mediated 18S pre-rRNA processing is essential for ribosome function and messenger RNA translation during maize seed development.

Detecting Resource Release Bugs with Analogical Reasoning

The resource release bugs are a common type of serious programming bug. However, it is hard to catch them by using static detection for the lacking of comprehensive prior knowledge about the release functions. In this paper, a resource release bug detection method is proposed by introducing analogical reasoning on word vectors. First, the functions of the target source code are encoded into word vectors by the word embedding technique in natural language processing. Second, a two-stage reasoning method is developed for automatically identifying unknown resource release functions according to a few well-known seed functions. 3CosAvg algorithm is employed for the first stage, and a new algorithm is designed for the latter, called 3CosAddExchange. Finally, the identified release functions are translated into static analysis rules to detect potential bugs. The experiment shows that the proposed method is effective and efficient for the large-scale software project. Five unknown resource release bugs are successfully detected in the Linux kernel and confirmed by kernel developers.

基于全基因组关联分析解析玉米籽粒大小的遗传结构

<p id="C3">Kernel size related traits are one of the important compounds of yield, and they are also complex quantitative traits regulated by multiple genes. Mining the key regulatory genes of maize kernel size related traits will help to improve the yield. In this study, 212 excellent maize inbred lines were selected as materials. The kernel length, kernel width, and kernel thickness were measured in 2018 and 2019, respectively, and we performed genome-wide association study (GWAS) based on 73,006 single nucleotide polymorphic (SNP) markers uniformly distributed in maize genome. Based on the FarmCPU algorithm, 47 SNP markers associated with kernel size related traits were detected on 10 chromosomes in maize. Combined with the public dynamic spatio-temporal transcriptional data of kernel development of B73 maize inbred line, 58 candidate genes related to kernel size were detected in the linkage disequilibrium (LD) region marked by significant SNP. The proteins encoded by candidate genes interacted with multiple proteins and participated in and regulated many biological processes closely related to kernel development. These results provide a new reference for understanding the molecular regulation mechanism of maize kernel development, improving kernel size and increasing crop yield.

Identification of a new mutant allele of ZmYSL2 that regulates kernel development and nutritional quality in maize.

The online version contains supplementary material available at 10.1007/s11032-022-01278-9.

Phenological growth stages of ‘Barcelona’ hazelnut (Corylus avellana L.) described using an extended BBCH scale

A wide range of hazelnut (Corylus avellana) cultivars are produced around the world. Cultivars are often listed by the time of bloom, from early to mid and late season. To date, phenological stages have been recorded using alphanumerical codes, although data analysis is difficult with such codes. This study converted the alphanumerical codes to fully numerical codes using the Biologische Bundesanstalt Bundessortenamt und Chemische Industrie (BBCH) scale. A hazelnut BBCH scale was created for the cultivar 'Barcelona', which is considered a reference for phenological stages. The scale was constructed with at least two digits (0 to 9) for the main growth stages and three digits for female flowering and fruit development. The first number indicates the general growth stage, the second number indicates the growth stage at a specific time, and the third digit, when present, indicates the proportion at that stage on the tree. The hazelnut BBCH scale describes in 38 stages within 7 of the 10 available stages. The BBCH stages used are 5 (inflorescence emergence), 6 (flowering), 0 (bud development), 1 (leaf development), 7 (fruit development), 8 (fruit ripening), and 9 (senescence). The hazelnut is unusual in that it flowers in winter. Thus, the scale was extended from flower initiation (spring to summer of the year before harvest), male and female flowering (winter before harvest) and bud and leaf development (spring before harvest). During the spring before harvest, and summer before harvest, fruit developmental stages and fruit ripening are monitored and finally, senescence finalises the hazelnut life cycle in autumn after the harvest. Thus, the BBCH hazelnut cycle has a duration of at least 18 months and gives a good idea of hazelnut development. Finally, this new scale will add new information on the kernel development stages which were not evaluated in the former phenological scale. It will help producers to have a better idea of the fruit ripening and potential harvest date.

Systematic transcriptomic and metabolomic analysis of walnut (Juglans regia L.) fruit to trace variations in antioxidant activity during ripening

Walnut is considered as a good source of antioxidants. However, the molecular mechanism for the composition and accumulation of antioxidant-related metabolites in walnut remains elusive. In this study, a comprehensive transcriptomic and metabolomic analysis was carried to reveal the metabolic dynamics, antioxidant activity variations and underlying regulatory networks during the development of walnut kernel. The results demonstrated that walnut kernel goes through the stages of cell division and proliferation, nutrient accumulation, and nutrient stabilization and maintenance, and the antioxidant activity first decreases and then increases during development. Metabolomic analysis identified a total of 176 metabolites in walnut. Hydrolyzed tannins (HT), coumarins and their derivatives (COA) are significantly positively correlated with the antioxidant activity. Phenylpropane metabolism is the key pathway for HT and COA synthesis, and CHI, CHS, F3H and UGT are the key regulatory enzymes. Sugars and organic acids provide energy and precursor for the accumulation of nutrients in walnut kernel through sugar metabolism and the tricarboxylic acid cycle (TCA). Large amounts of amino acids are accumulated at the nutrient accumulation stage, providing precursors for the formation of proteins and flavonoids during the ripening of walnut. Our results provide new insights into the metabolic regulation of antioxidant activity during walnut ripening.

Automatic Permission Check Analysis for Linux Kernel

Permission checks play an essential role in operating system security by providing access control to privileged functionalities. However, it is challenging for kernel developers to scalably verify the soundness of existing checks due to the large codebase and complexity of the kernel. In fact, Linux kernel contains millions of lines of code with hundreds of permission checks, and even worse its complexity is fast-growing. This paper presents PeX, a static permission check error detector for Linux, which takes as input a kernel source code and reports any missing, inconsistent, and redundant permission checks. PeX uses KIRIN (Kernel InteRface based Indirect call aNalysis), a novel, precise, and scalable indirect call analysis technique. Over the interprocedural control flow graph built by KIRIN, PeX automatically identifies permission checks and infers the mappings between permission checks and privileged functions. For each privileged function, PeX examines all possible paths to the function to check if necessary permission checks are correctly enforced. We evaluated PeX on the latest stable Linux kernel v4.18.5 for three types of permission checks: Discretionary Access Controls (DAC), Capabilities, and Linux Security Modules (LSM). PeX reported 45 new permission check errors, 17 of which have been confirmed by the kernel developers.

Ignition and Development of Flame Kernel Formed by Nano-Second Repetitively Pulsed Discharges (NRPDs) in the Quiescent Lean Premixed Mixture

Ignition and Development of Flame Kernel Formed by Nano-Second Repetitively Pulsed Discharges (NRPDs) in the Quiescent Lean Premixed Mixture