Kernel Development Research Articles

VFS over the Years: An Efficient Change Log and System Call for Kernel Developers

“The Linux Kernel is getting bloated and huge, it’s a problem. Sometimes it's a bit sad that we are definitely not the streamlined, small, hyper-efficient kernel that I envisioned 15 years ago … The kernel is huge and bloated” – Linus Torvalds, Linuxcon2009 (Roundtable - The Linux Kernel: Straight From the Source). [1] The Linux Kernel is getting large day by day, both in terms of lines of code and complexity of features and functions. This includes rapid changes in naming conventions of kernel functions, variables and even the flow of data within the code. Moreover, these changes are not well supported by adequate documentation. These issues account to incremental difficulties faced by developers of system code across the globe. This paper is a study of internal working and changes of virtual File System specific code of Linux kernel versions 2.4, 2.6. and 3.0. We have tried to introduce various changes and new addition of several features of the Linux kernel. This survey regarding virtual file system among various kernel versions may play an important role for system developers during system development to gather information about file system in any specific or several kernel versions.

Numerical modeling of ignition enhancement by repetitive nanosecond discharge in a hydrogen/air mixture II: forced ignition

Non-equilibrium plasma has promising applications in combustion enhancement. In this study, 1D simulations are conducted for the forced ignition process using non-equilibrium plasma generated by repetitively pulsed nanosecond discharge (NSD). The ignition kernel is induced by a discharge area with NSD and it develops and propagates in a static stoichiometric hydrogen/air mixture. The objective is to assess how the characteristics of NSD affect the ignition delay time and ignition kernel development during the forced ignition process. Similar to the homogeneous ignition considered in part I, the forced ignition process is found to be strongly affected by the pulse number, discharge frequency, discharge radius, total input energy, and input energy per pulse of NSD. For a fixed input energy per pulse, the ignition delay time decreases and the propagation speed of the initial ignition kernel increases with the pulse number, discharge frequency and discharge radius. However, for a fixed total input energy, the ignition delay time increases and the propagation speed of the initial ignition kernel decreases with the pulse number. Furthermore, it is found that the promotion of ignition kernel development and propagation in the forced ignition by NSD are mainly due to the kinetic effect rather than the thermal effect.

Maize transcription factor ZmBES1/BZR1-5 positively regulates kernel size.

The BES1/BZR1 transcription factors regulate the expression of genes responsive to brassinosteroids and play pivotal roles in plant development, but their role in regulating kernel development in maize remains unclear. In this study, we found that ZmBES1/BZR1-5 positively regulates kernel size. Association analysis of candidate genes in 513 diverse maize inbred lines indicated that three SNPs related to ZmBES1/BZR1-5 were significantly associated with kernel width and whilst four SNPs were related to 100-kernel weight. Overexpression of ZmBES1/BZR1-5 in Arabidopsis and rice both significantly increased seed size and weight, and smaller kernels were produced in maize Mu transposon insertion and EMS mutants. The ZmBES1/BZR1-5 protein locates in the nucleus, contains bHLH and BAM domains, and shows no transcriptional activity as a monomer but forms a homodimer through the BAM domain. ChIP-sequencing analysis, and yeast one-hybrid and dual-luciferase assays demonstrated that the protein binds to the promoters of AP2/EREBP genes (Zm00001d010676 and Zm00001d032077) and inhibits their transcription. cDNA library screening showed that ZmBES1/BZR1-5 interacts with casein kinase II subunit β4 (ZmCKIIβ4) and ferredoxin 2 (ZmFdx2) in vitro and in vivo, respectively. Taken together, our study suggests that ZmBES1/BZR1-5 positively regulates kernel size, and provides new insights into understanding the mechanisms of kernel development in maize.

ZmSKS13, a cupredoxin domain-containing protein, is required for maize kernel development via modulation of redox homeostasis.

The SKU5 similar (SKS) genes encode a family of multi-copper-oxidase-like proteins with cupredoxin domains similar to those in laccase and ascorbate oxidase. Although SKS proteins are known to function in root growth and cotyledon vascular patterning in Arabidopsis, their role in plant reproductive processes is poorly understood. Here, we identified a seed mutant of maize (Zea mays), generated by ethyl methane sulfonate (EMS) mutagenesis, that we designated defective kernel-zk1 (dek-zk1). The mutant produced small, shriveled kernels with an aberrant basal endosperm transfer layer (BETL) and placento-chalazal (PC) layer and irregular starch granules. Map-based cloning revealed that Dek-zk1 encodes an SKU5 similar 13 (GenBank: ONM36900.1), so it was named ZmSKS13. ZmSKS13 comprises a paralogous pair with Zm00001d012524, but the transcript abundance of ZmSKS13 in developing kernels is 15 times higher than that of Zm00001d012524, resulting in dek-zk1 mutation conveying a distinct kernel phenotype. ZmSKS13 loss of function led to overaccumulation of reactive oxygen species (ROS) and severe DNA damage in the nucellus and BETL and PC layer cells, and exogenous antioxidants significantly alleviated the defects of the mutant kernels. Our results thus demonstrate that ZmSKS13 is a novel regulator that plays a crucial role in kernel development in maize through the modulation of ROS homeostasis.

Creep mathematical model on the example of early age concrete

The objective of the study is development of a creep kernel recording form, which allows obtaining representations for creep curves calculation. Based on the elastic-creeping body theory a possibility of the high-rate creep movement analytical study has been shown. A creep kernel, which contains a formula to describe the aging material properties, has been built. Essential stages of the proposed creep kernel formation have been given. The correspondence of the proposed calculations to real processes has been proved by a comparison with experimental data. In the numerical implementation, decomposition of integration elements into power series has been used. A possibility of calculating functions for a long time interval has been shown. Creep kernel parameters have been determined on the basis of experimental data of early age concrete samples by minimizing the standard deviation of theoretical and empirical values.

Flame kernel development by laser ignition in methane/air premixed gas under reduced pressure condition

Flame kernel development by laser ignition in methane/air premixed gas under reduced pressure condition

Cytokinin activity during early kernel development corresponds positively with yield potential and later stage ABA accumulation in field-grown wheat (Triticum aestivum L.).

Early cytokinin activity and late abscisic acid dynamics during wheat kernel development correspond to cultivars with higher yield potential. Cytokinins represent prime targets for marker development for wheat breeding programs. Two major phytohormone groups, abscisic acid (ABA) and cytokinins (CKs), are of crucial importance for seed development. Wheat (Triticum aestivum L.) yield is, to a high degree, determined during the milk and dough stages of kernel development. Therefore, understanding the hormonal regulation of these early growth stages is fundamental for crop-improvement programs of this important cereal. Here, we profiled ABA and 25 CK metabolites (including active forms, precursors and inactive conjugates) during kernel development in five field-grown wheat cultivars. The levels of ABA and profiles of CK forms varied greatly among the tested cultivars and kernel stages suggesting that several types of CK metabolites are involved in spatiotemporal regulation of kernel development. The seed yield potential was associated with the elevated levels of active CK levels (tZ, cZ). Interestingly, the increased kernel cZ levels were followed by higher ABA production, suggesting there is an interaction between these two phytohormones. Furthermore, we analyzed the expression patterns of representatives of the four main CK metabolic gene families. The unique transcriptional patterns of the IPT (biosynthesis) and ZOG (reversible inactivation) gene family members (GFMs) in the high and low yield cultivars additionally indicate that there is a significant association between CK metabolism and yield potential in wheat. Based on these results, we suggest that both CK metabolites and their associated genes, can serve as important, early markers of yield performance in modern wheat breeding programs.

Changes in the phenolic compound content and antioxidant activity in developmental maize kernels and expression profiles of phenolic biosynthesis-related genes

Phenolic compounds have various nutritional and functional properties, especially antioxidant activity. The objective of this study was to explore the relationship between the phenolic compound accumulation, antioxidant property and gene expression during maize kernel development. In this study, we explored the effects of developmental stage on the accumulation of phenolic compounds and their antioxidant activities. The expression levels of genes involved in phenolic biosynthesis were also studied. The results showed that the total phenolic content (TPC) and total anthocyanin content (TAC) were gradually increased from 15 to 48 days after pollination (DAP), whereas the total flavonoid content (TFC) decreased continuously. The antioxidant activity of maize kernels was increased gradually and positively associated with TPC. ZmCHSs in flavonoid biosynthetic pathway played important roles for total flavonoid accumulation at both early and later development stages. The expression pattern of ZmANS corresponded to the accumulation of total anthocyanin during kernel development. These results revealed that developmental stage affected the accumulation of different phenolic compounds, antioxidant activity and related gene expression. The antioxidant activity of maize kernels was dependent on the total phenolic accumulation which was related to the expression profiles of the genes participated in phenolic synthesis.

Analysis of preharvest meteorological conditions in relation to concentration of fumonisins in kernels of two genetically different maize hybrids

The effects of meteorological conditions around silking (Si) and physiological maturity (PM) on production of fumonisins (FB=FB1 + FB2) in maize kernels were analyzed. Kernel FB contents were determined on kernel samples collected from an experimental susceptible hybrid (n = 35) and a Bt commercial hybrid (n = 23) planted in several growing seasons/sites from the Argentinean Pampas. Considering the effect of genetic divergence of the two maize hybrids, total kernel FB concentrations (n = 52) binary coded, were predicted appropriately by weather-based logistic regression models but underestimated in some samples severely contaminated with FB. After removing these misclassified cases that registered maximum values of a drought-heat stress index (DI) calculated over 30 days around Si, and weather conditions (assessed by weather interactive components) conducive to infection/production of FB in PM, new logistic models were fitted. These new models improved their predictive ability indices. It was remarkable a model including the discrete genetic variable and the weather variable associated with the simultaneous occurrence of precipitation, temperature between 19.5–33 °C and relative humidity >70%, required for fungal infection in Si. Models that also included weather variables calculated in PM and associated with the kernel drying rate and fungal infection, did not result in better prediction outcomes. Opposite to the general trend, the occurrence of both severe heat-drought stress around Si and favorable weather around PM led to high kernel FB contents. We hypothesize that husk shortening by stress at silking might expose ears, promoting Fusarium verticillioides colonization/FB synthesis in late stages of kernel development and maturity, whenever favorable environmental conditions for both processes prevail.

Spatio-temporal evolution of cavity ignition in supersonic flow

Successful ignition in the recirculating flow of a scramjet flame holder can be highly dependent upon the location of energy deposition because of the spatial variation of fuel concentration and flow properties. The current work experimentally investigated ignition processes when energy was deposited (∼100 mJ) via a spark discharge at four locations in the base of a cavity or by laser-induced breakdown in a Mach 2 flow with a stagnation temperature and pressure of 590 K and 483 kPa, respectively. The cavity was directly fueled with ethylene injection. The time dependent heat release was imaged at 40,000 frames per second and fuel concentration and distribution measurements were taken in the cavity prior to ignition. The average fuel concentration at the lean and rich ignition limits near the energy deposition locations measured 4.4–9.3% (Φ= 0.75 to 1.47). Energy deposition near the cavity step resulted in near immediate ignition kernel development and rapid achievement of self-sustained flame propagation in the front of the cavity, often faster than the bulk recirculation time of the cavity, leading to a spike in heat release. Energy deposition away from the cavity step region led to competition between local flow velocity, fuel concentration, and flame propagation rates. Ignition kernels formed along the floor of the cavity towards the closeout ramp and were rapidly advected towards the cavity step region before flame propagation could ensue. The fastest and most robust ignition events for all fueling cases showed rapid spanwise flame propagation near the cavity step.

Glycolysis stimulation and storage protein accumulation are hallmarks of maize (Zea mays L.) grain filling

Maize (Zea mays L.) is a major dietary source of human caloric intake. Grain filling, the developmental stage of the seed during which starch and proteins accumulate, is of great interest in plant biology and agronomy. However, proteomic datasets covering maize seed development, especially during grain filling, are much scarcer than transcriptomic datasets, largely due to the labor-intensive and costly nature of the large-scale analysis required for proteomics. Here, we searched for proteins that showed changes in abundance during four time-points covering the middle stages of grain filling by two-dimensional electrophoresis, MALDI-TOF, and database searches. We detected 1384 protein spots, of which 48 exhibited differential accumulation during grain filling. Of those, we identified the underlying protein for 32 spots: they included enzymes of carbohydrate metabolism, stress-related proteins, and storage proteins, the latter of which represented 34% of all changing proteins during grain filling. Proteins related to carbohydrate metabolism reached their maximum accumulation around 15–20 days after pollination (DAP) and subsequently dropped until 30 DAP. The rise of stress-related proteins such as heat shock proteins demonstrated their involvement in grain filling and seed maturation. This study catalogues the proteome changes during grain filling and provides basic but critical information regarding the biological changes during maize kernel development.

Effect of CO2 dilution on forced ignition and development of CH4/air ignition kernels

Reliable ignition of reactant mixtures containing combustion products is important to the function of many practical combustion devices. Prior work has considered the influence of CO2 on ignition delay times and laminar flame speeds. This work examines the effects of dilution with CO2 on forced ignition and development of ignition kernels in CH4/air mixtures. Ignition kernels were initiated by a high voltage spark discharge in CH4/air/diluent mixtures with a bulk velocity of 5 m/s and with 0.7 ≤ Φ ≤ 0.8. Ignition probabilities and kernel growth rates were determined from radiation intensity measurements collected using a Telops MS-IR FAST infrared camera. Nitrogen was used as an inert in a subset of conditions to facilitate identifying changes in chemistry associated with dilution by CO2. Chemistry effects of diluents on ignition were isolated by examining undiluted, N2 diluted, and CO2 diluted flows with equivalent adiabatic flame temperatures. Dilution with CO2 reduced the probability of ignition relative to undiluted and N2 diluted conditions with the same adiabatic flame temperature. Ignition kernels diluted with CO2 also tended to be smaller than those initiated in both undiluted and N2 diluted mixtures, with reduced growth rates.

Phenotype analysis and gene mapping of small kernel 7 (<italic>smk7</italic>) mutant in maize

<p indent=0mm>In this study, a stable small kernel mutant, named <italic>small kernel 7 </italic>(<italic>smk7</italic>), was isolated from ethylmethane sulfonate (EMS) mutagenesis of maize inbred line B73. Compared with wild type, the <italic>smk7 </italic>mutants showed smaller kernel size, defective embryo and endosperm development and a significant decrease in 100-kernel weight. The <italic>smk7</italic> kernels showed a low level of germination rate at 10% and cannot grow into normal plants. No significant changes were detected in protein, starch and oil content between mature wild type and <italic>smk7</italic> kernels, but the starch grains became significantly smaller and irregular in <italic>smk7</italic> kernels compared with wild type. The <italic>smk7</italic> kernels could be clearly distinguished from the wild type as early as 12 days after pollination (DAP), on the basis of their smaller and emptier phenotype. Microscopic inspection of the paraffin sections revealed that the development of embryo and endosperm were delayed, and the cell wall in growth in basal endosperm transfer layers (BETL) were arrested in <italic>smk7</italic> compared with wild type. The F₂ populations with multiple backgrounds were constructed by crossing heterozygous plants (+/<italic>smk7</italic>) with several other inbred lines. Genetic analysis showed that the mutant phenotype was controlled by a single recessive gene. Based on genotyping by target sequencing (GBTS) strategy, the <italic>SMK7 </italic>was initially mapped on the short arm of chromosome 2. The fine mapping results suggested that <italic>SMK7</italic> was located between markers RM1433917 and RM1535316, with a physical distance of 120 kb. There were eight protein-coding genes in this region. This study laid a foundation for further genes cloning and research of the<italic> SMK7 </italic>function in regulating maize kernel development.

RCU Usage In the Linux Kernel

Read-copy update (RCU) is a scalable high-performance synchronization mechanism implemented in the Linux kernel. RCU's novel properties include support for concurrent forward progress for readers and writers as well as highly optimized inter-CPU synchronization. RCU was introduced into the Linux kernel eighteen years ago and most subsystems now use RCU. This paper discusses the requirements that drove the development of RCU, the design and API of the Linux RCU implementation, and how kernel developers apply RCU.

Gas dynamic regimes observed in dual-pulse laser ignition

A numerical study of the gas dynamics induced by a dual-pulse laser pre-ionization plasma used in laser ignition applications is presented herein. Past experimental observations have revealed important differences in the gas dynamics of the dual-pulse plasma, generated by overlapping a pair of ultraviolet (UV) and near-infrared (NIR) pulses, as compared to those of single-pulse (typically near-infrared) laser breakdown that has been more commonly studied. The simulation results reported here show that the dual-pulse pre-ionization scheme can lead to various gas dynamic regimes depending on the axial offset of the focal points of the two beams along the optical axis. If the UV and NIR pulses are perfectly overlapped (no offset) the energy deposition is uniform along the optical axis, leading to the formation of a toroidal structure in the post-discharge cooling phase. Alternatively, if the NIR energy addition pulse is focused with a small axial offset, (i.e., upstream or downstream of the UV pre-ionization pulse by ~0.5 mm) then an asymmetric torus forms that exhibits a third lobe which propagates away from the main kernel (to the side where the NIR was focused). Finally, if the two beams are focused with a larger offset of ~2.5 mm (weaker coupling), then another regime with a fourth lobe can arise. The four main flow regimes revealed from the model are in agreement with OH* experimental chemiluminescence images. These flow regimes influence the development of the early flame kernels, therefore playing an important role in practical laser ignition applications.

Effects of Biogas Composition on the Edge Flame Propagation in Igniting Turbulent Mixing Layers

Three-dimensional compressible Direct Numerical Simulations have been used to investigate the localised forced ignition of statistically planar biogas/air mixing layers for different levels of turbulence intensity and biogas composition. The biogas is represented by a hbox {CH}_4/hbox {CO}_2 mixture and a two-step mechanism capturing the variation of the unstrained laminar flame speed with equivalence ratio and hbox {CO}_2 dilution was used. The mixture composition was found to significantly affect the flame kernel development which was reflected in the diminished growth rate of the burned gas volume with increasing hbox {CO}_2 dilution. A successful ignition of hbox {CH}_4/hbox {CO}_2/air mixing layer gives rise to a tribrachial flame structure involving fuel-rich and lean premixed branches on either side of the diffusion flame stabilised on the stoichiometric mixture fraction iso-surface. The most probable edge flame speed decreases in time and converges to a value that is at most equal to its laminar theoretical limit, and can even locally become negative for large values of the dilution and/or turbulence intensity. The decomposition of the edge flame speed showed a negligible or negative contribution of the mixture fraction surface displacement speed, while the displacement speed of the fuel mass fraction surface appeared as the dominant contributor. Finally, the edge flame speed dependences to the fuel mass fraction and mixture fraction gradients, fuel mass fraction iso-surface curvature and tangential strain rate have been analysed and found, within the dilution values considered, qualitatively similar to those of undiluted mixtures regardless of the amount of hbox {CO}_2, although quantitative differences were observed.

A proteomic analysis of grain yield-related traits in wheat.

Grain yield, which is mainly contributed by tillering capacity as well as kernel number and weight, is the most important trait to plant breeders and agronomists. Label-free quantitative proteomics was used to analyse yield-contributing organs in wheat. These were leaf sample, tiller initiation, spike initiation, ovary and three successive kernel development stages at 5, 10 and 15 days after anthesis (DAA). We identified 3182 proteins across all samples. The largest number was obtained for spike initiation (1673), while the smallest was kernel sample at 15 DAA (709). Of the 3182 proteins, 296 of them were common to all seven organs. Organ-specific proteins ranged from 148 in ovary to 561 in spike initiation. When relative protein abundances were compared to that of leaf sample, 347 and 519 proteins were identified as differentially abundant in tiller initiation and spike initiation, respectively. When compared with ovary, 81, 35 and 96 proteins were identified as differentially abundant in kernels sampled at 5, 10 and 15 DAA, respectively. Our study indicated that two Argonaute proteins were solely expressed in spike initiation. Of the four expansin proteins detected, three of them were mainly expressed during the first 10 days of kernel development after anthesis. We also detected cell wall invertases and sucrose and starch synthases mainly during the kernel development period. The manipulation of these proteins could lead to increases in tillers, kernels per spike or final grain weight, and is worth exploring in future studies.

Composition analysis of lysine, tryptophan and provitamin-A during different stages of kernel development in biofortified sweet corn

Traditional sweet corn is poor in nutritional quality. Here, a set of biofortified sweet corn hybrids were analyzed for nutritional traits at 20-, 24- and 28- days after pollination (DAP) under three sowing dates. The biofortified hybrids possessed significantly higher lysine (0.34 %), tryptophan (0.08 %), β-carotene (BC: 13.77 μg/g), β-cryptoxanthin (BCX: 11.19 μg/g) and provitamin-A (proA: 19.38 μg/g) over traditional yellow sweet corn (0.21 %, 0.03 %, 1.96 μg/g, 2.32 μg/g and 3.12 μg/g). Sowing time, harvest time and their interactions had significant influence on nutritional traits. Decreasing trend of accumulation for lysine (0.367 %, 0.345 % and 0.315 %), tryptophan (0.086 %, 0.078 % and 0.068 %), BC (15.18 μg/g, 14.00 μg/g and 12.12 μg/g), BCX (12.28 μg/g, 11.48 μg/g and 9.82 μg/g) and proA (21.32 μg/g, 19.74 μg/g and 17.07 μg/g) was observed at 20-, 24- and 28-DAP, respectively. However, mean brix attained the peak at 24-DAP (18.53 %), followed by 20-DAP (17.86 %) and 28-DAP (17.60 %). Considering both nutrition and sweetness, 20-DAP was the best suitable time for harvesting of sweet corn ears. Nutritional traits had higher concentration with delay in sowing time. This is the first report on accumulation of lysine, tryptophan and proA at different stages of kernel development in biofortified sweet corn.

Dynamic proteome changes of wheat developing grains in response to water deficit and high-nitrogen fertilizer conditions

This study investigated grain proteomic profiles in response to water deficit, high nitrogen (N) fertilizer, and their combined treatments in elite Chinese bread wheat cultivar Jingdong 17, using a two-dimensional difference gel electrophoresis (2D-DIGE)-based approach. Water deficit negatively affected the main agronomic traits of wheat and grain yield, while high-N fertilizer had the opposite effects. The application of a high-N fertilizer under water deficit conditions moderately improved kernel development and grain yield. 2D-DIGE led to the identification of 124 differentially accumulated protein (DAP) spots during five different grain developmental stages, corresponding to 97 unique proteins. The more significant changes of DAPs occurred at 10–20 days after flowering. DAPs were involved in carbohydrate metabolism, protein turnover, protein folding, cell cycle control, stress response, nitrogen metabolism, photosynthesis, and energy metabolism. In particular, water deficit caused a significant downregulation of proteins involved in starch biosynthesis, whereas high-N fertilizer led to a significant upregulation of proteins involved in nitrogen metabolism, carbohydrate metabolism, and starch biosynthesis. The combined treatment resulted in a moderate upregulation of DAPs related to carbohydrate metabolism, starch biosynthesis, and nitrogen metabolism. Our results indicated that high-N fertilization could alleviate yield loss caused by water deficit by promoting the accumulation of proteins involved in nitrogen and carbohydrate metabolism.

The role of differential diffusion during early flame kernel development under engine conditions - part I: Analysis of the heat-release-rate response

Although experimental evidence for the correlation between early flame kernel development and cycle-to-cycle variations (CCV) in spark ignition (SI) engines was provided long ago, there is still a lack of fundamental understanding of early flame/turbulence interactions, and accurate models for full engine simulations do not exist. Since the flame kernel is initiated with small size, i.e. with large positive curvature, differential diffusion is expected to severely alter early flame growth in non-unity-Lewis-number (Le ≠ 1) mixtures as typically used in engines. In this work, a DNS database of developing iso-octane/air flame kernels and planar flames has been established with flame conditions representative for stoichiometric engine part-load operation. Differential diffusion effects on the global heat release rate are analyzed by relating the present findings to equivalent flames computed in the Le=1 limit. It is shown that in the early kernel development phase, the normal propagation velocity is significantly reduced with detrimental consequences on the global burning rate of the flame kernel. Besides this impact on the overall mass burning rate, the initial production of flame surface area by the normal propagation term in the flame area balance equation is noticeably reduced. By using the optimal estimator concept, it is shown that strong fluctuations in local heat release rate inherent to Le ≠ 1 flames in the thin reaction zones regime are mainly contained in the parameters local equivalence ratio, enthalpy, and H-radical mass fraction. Differential diffusion couples the evolution of these parameters to the unsteady flame geometry and structure, which is analyzed in Part II of the present study (Falkenstein et al., Combust. Flame, 2020).