• Journal of Mechanical Science and Technology
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• v.20 no.9
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• pp.1449-1458
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• 2006

Controlled Auto-ignition (CAI) combustion processes can be broadly divided between a CAI process that is applied to four-cycle engines and a CAI process that is applied to two-cycle engines. The former process is generally referred to as Homogeneous Charge Compression Ignition (HCCI) combustion and the later process as Active Thermo-Atmosphere Combustion (ATAC) The region of stable engine operation differs greatly between these two processes, and it is thought that the elucidation of their differences and similarities could provide useful information for expanding the operation region of HCCI combustion. In this research, the same two-cycle engine was operated under both the ATAC and HCCI combustion processes to compare their respective combustion characteristics. The results indicated that the ignition timing was less likely to change in the ATAC process in relation to changes in the fuel octane number than it was in the HCCI combustion process.

• International Journal of Automotive Technology
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• v.8 no.2
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• pp.137-147
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• 2007

Homogenous Charge Compression Ignition (HCCI) combustion systems can be broadly divided for the process applied to 4-stroke and 2-stroke engines. The former process is often referred to as simply HCCI combustion and the latter process as Active Thermo-Atmosphere Combustion (ATAC). The region of stable engine operation tends to differ greatly between the two processes. In this study, it was shown that the HCCI combustion process of a 4-stroke engine, characterized by the occurrence of autoignition under a high compression ratio, a lean mixture and wide open throttle operation, could be simulated by operating a 2-stroke engine at a higher compression ratio. On that basis, a comparison was made of the combustion characteristics of high-compression-ratio HCCI combustion and ATAC, characterized as autoignited combustion in the presence of a large quantity of residual gas at a low compression ratio and part throttle. The results showed that one major difference between these two combustion processes was their different degrees of susceptibility to the occurrence of cool flame reactions. Compared with high-compression-ratio HCCI combustion, the ignition timing of ATAC tended not to change in relation to different fuel octane numbers. Furthermore, when internal EGR was applied to high-compression-ratio HCCI combustion, it resulted in combustion characteristics resembling ATAC. Specifically, as the internal EGR rate was increased, the ignition timing showed less change in relation to changes in the octane number and the region of stable engine operation also approached that of ATAC.

• Molecules and Cells
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• v.45 no.5
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• pp.343-352
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• 2022

The advent of the assay for transposase-accessible chromatin using sequencing (ATAC-seq) has shown great potential as a leading method for analyzing the genome-wide profiling of chromatin accessibility. A comprehensive reference to the ATAC-seq dataset for disease progression is important for understanding the regulatory specificity caused by genetic or epigenetic changes. In this study, we present a genome-wide chromatin accessibility profile of 44 liver samples spanning the full histological spectrum of nonalcoholic fatty liver disease (NAFLD). We analyzed the ATAC-seq signal enrichment, fragment size distribution, and correlation coefficients according to the histological severity of NAFLD (healthy control vs steatosis vs fibrotic nonalcoholic steatohepatitis), demonstrating the high quality of the dataset. Consequently, 112,303 merged regions (genomic regions containing one or multiple overlapping peak regions) were identified. Additionally, we found differentially accessible regions (DARs) and performed transcription factor binding motif enrichment analysis and de novo motif analysis to determine new biomarker candidates. These data revealed the gene-regulatory interactions and noncoding factors that can affect NAFLD progression. In summary, our study provides a valuable resource for the human epigenome by applying an advanced approach to facilitate diagnosis and treatment by understanding the non-coding genome of NAFLD.

• Journal of Genetic Medicine
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• v.20 no.1
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• pp.1-5
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• 2023

Until now, rare disease studies have mainly been carried out by detecting simple variants such as single nucleotide substitutions and short insertions and deletions in protein-coding regions of disease-associated gene panels using diagnostic next-generation sequencing in association with patient phenotypes. However, several recent studies reported that the detection rate hardly exceeds 50% even when whole-exome sequencing is applied. Therefore, the necessity of introducing whole-genome sequencing is emerging to discover more diverse genomic variants and examine their association with rare diseases. When no diagnosis is provided by whole-genome sequencing, additional omics techniques such as RNA-seq also can be considered to further interrogate causal variants. This paper will introduce a description of these multi-omics techniques and their applications in rare disease studies.

• Journal of ILASS-Korea
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• v.25 no.4
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• pp.188-195
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• 2020

To meet stringent emission regulations of automotive engines, fuel injection control techniques have advanced based on reliable and fast computing prediction models. This study aims to develop a reliable lightweight prediction model of fuel injection rates using a small number of input parameters and based on simple fluid dynamic theories. The prediction model uses the geometry of the injector nozzle, needle motion data, injection conditions and the fuel properties. A commercial diesel injector and US No. 2 diesel were used as the test injector and fuel, respectively. The needle motion data were measured using X-ray phase-contrast imaging technique under various fuel injection pressures and injection pulse durations. The actual injector rate profiles were measured using an injection rate meter for the validation of the model prediction results. In the case of long injection durations with the steady-state operation, the model prediction results showed over 99 % consistency with the measurement results. However, in the case of short injection cases with the transient operation, the prediction model overestimated the injection rate that needs to be further improved.

• Molecules and Cells
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• v.44 no.9
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• pp.627-636
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• 2021

The three-dimensional organization of chromatin and its time-dependent changes greatly affect virtually every cellular function, especially DNA replication, genome maintenance, transcription regulation, and cell differentiation. Sequencing-based techniques such as ChIP-seq, ATAC-seq, and Hi-C provide abundant information on how genomic elements are coupled with regulatory proteins and functionally organized into hierarchical domains through their interactions. However, visualizing the time-dependent changes of such organization in individual cells remains challenging. Recent developments of CRISPR systems for site-specific fluorescent labeling of genomic loci have provided promising strategies for visualizing chromatin dynamics in live cells. However, there are several limiting factors, including background signals, off-target binding of CRISPR, and rapid photobleaching of the fluorophores, requiring a large number of target-bound CRISPR complexes to reliably distinguish the target-specific foci from the background. Various modifications have been engineered into the CRISPR system to enhance the signal-to-background ratio and signal longevity to detect target foci more reliably and efficiently, and to reduce the required target size. In this review, we comprehensively compare the performances of recently developed CRISPR designs for improved visualization of genomic loci in terms of the reliability of target detection, the ability to detect small repeat loci, and the allowed time of live tracking. Longer observation of genomic loci allows the detailed identification of the dynamic characteristics of chromatin. The diffusion properties of chromatin found in recent studies are reviewed, which provide suggestions for the underlying biological processes.

• Molecules and Cells
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• v.43 no.12
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• pp.1011-1022
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• 2020

Cell type specification is a delicate biological event in which every step is under tight regulation. From a molecular point of view, cell fate commitment begins with chromatin alteration, which kickstarts lineage-determining factors to initiate a series of genes required for cell specification. Several important neuronal differentiation factors have been identified from ectopic over-expression studies. However, there is scarce information on which DNA regions are modified during induced pluripotent stem cell (iPSC) to neuronal progenitor cell (NPC) differentiation, the cis regulatory factors that attach to these accessible regions, or the genes that are initially expressed. In this study, we identified the DNA accessible regions of iPSCs and NPCs via the Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq). We identified which chromatin regions were modified after neuronal differentiation and found that the enhancer regions had more active histone modification changes than the promoters. Through motif enrichment analysis, we found that NEUROD1 controls iPSC differentiation to NPC by binding to the accessible regions of enhancers in cooperation with other factors such as the Hox proteins. Finally, by using Hi-C data, we categorized the genes that directly interacted with the enhancers under the control of NEUROD1 during iPSC to NPC differentiation.

• Geomechanics and Engineering
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• v.29 no.4
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• pp.421-434
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• 2022

In the present study, reference samples were prepared using ore preparation facility tailings taken from the copper mine (Kure, Kastamonu), Portland cement (PC) in certain proportions (3 wt%, 5 wt%, 7 wt%, 9wt% and 11 wt%), and water. Then natural zeolite taken from the Bigadic Region was mixed in certain proportions (10 wt%, 20 wt%, 30 wt% and 40 wt%) for each cement ratio, instead of the PC, to prepare zeolite-substituted CPB samples. Thus, the effect of using Zeolite instead of PC on CPB's strength was investigated. The obtained CPB samples were kept in the curing cabinet at a temperature of 25℃ and at least 80% humidity, and they were subjected to the Uniaxial Compressive Strength (UCS) test at the end of the curing periods of 3, 7, 14, 28, 56, and 90 days. Except for the 3 wt% cement ratio, zeolite substitution was observed to increase the compressive strength in all mixtures. Also, the liquefaction risk limit for paste backfill was achieved for all mixtures, and the desired strength limit value (0.7 MPa) was achieved for all mixtures with 28 days of curing time and 7 wt%, 9 wt%, 11 wt% cement ratios and 5% cement - 10% zeolite substituted mixture. Moreover, the limit value (4 MPa) required for use as roof support was obtained only for mixtures with 11% cement - 10% and 20% zeolite content. Generally, zeolite substitution seems to be more effective in early strength (up to 28th day). It has been determined that the long-term strength losses of zeolite-substituted paste backfill mixtures were caused by the reaction of sulfate and hydration products to form secondary gypsum, ettringite, and iron sulfate.