• Genomics & Informatics
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• 제15권1호
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• pp.11-18
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• 2017

Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, 'ChIPseeker' performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git.

• Preventive Nutrition and Food Science
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• 제9권1호
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• pp.98-106
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• 2004

Tomatoes and tomato products are the major source of lycopene in the diet. The bioavailability of lycopene is different in raw tomatoes compared to processed tomato products. This is due to the chemical and physical properties of the different lycopene isomers. All-trans-lycopene is found in raw tomatoes and is a poor bioavailable source, whereas, processed tomato products are more bioavailable because they contain more cis-isomers. Heat and mechanical processing of tomatoes induces rupture of the cell walls, thereby releasing lycopene from its food matrix. Heat processing also induces cis-trans isomerization and disrupts protein-carotenoid complexes. Many dietary components also impact lycopene bioavailability, like the amount and type of fat present with the intake and processing of tomato products, the amount and type of fiber present, and the interaction between carotenoids. Fundamentally, anything that enhances formation and incorporation of lycopene in bile acid micelles increases bioavailability, and the opposite is true in that anything that interferes with micelle formation decreases bioavailability.

• Asian Pacific Journal of Cancer Prevention
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• 제14권5호
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• pp.2765-2769
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• 2013

Background: A close association between patterns identified by magnifying narrow-band imaging (M-NBI) and histological type has been described. M-NBI patterns were also recently reported to be related to the mucin phenotype; however, detials remain unclear. Materials and Methods: We investigated the cellular differentiation of gastric cancer lesions, along with their mucosal distribution observed by M-NBI. Ninety-seven depressed-type early gastric cancer lesions (74 differentiated and 23 undifferentiated adenocarcinomas) were visualized by M-NBI. Findings were divided into 4 patterns based on abnormal microvascular architecture: a chain loop pattern (CLP), a fine network pattern (FNP), a corkscrew pattern (CSP), and an unclassified pattern. Mucin phenotypes were judged as gastric (G-type), intestinal (I-type), mixed gastric and intestinal (M-type), and null (N-type) based on 4 markers (MAC5AC, MUC6, MUC2, and CD10). The relationship of each pattern of microvascular architecture with organoid differentiation indicated by cancer cell differentiation and its distribution in each histological type of early gastric cancer was investigated. Results: All CLP and FNP lesions were differentiated. The cancer cell distribution showed organoid differentiation in 84.2% (16/19) and 61.1% (22/36) of the two types of lesions, respectively, and there was a significant difference from the unclassified pattern with organoid differentiation (p<0.001). Almost all (94.7%; 18/19) CSP lesions were undifferentiated, and organoid differentiation was observed in 72.2% (13/18). There was a significant difference from the unclassified pattern with organoid differentiation (p<0.05). Conclusions: Cellular differentiation and distribution are associated with microvascular architecture observed by M-NBI.

• IMMUNE NETWORK
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• 제11권1호
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• pp.68-78
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• 2011

Background: Graft-versus-host disease (GVHD) is a huddle for success of hematopoietic stem cell transplantation. In this study, effects of irradiation dose on immune kinetics of GVHD were investigated using B6 ${\rightarrow}$ BALB.B system, a mouse model for GVHD after MHC-matched allogeneic transplantation. Methods: BALB.B mice were transplanted with bone marrow and spleen cells from C57BL/6 mice after irradiation with different doses. Leukocytes residing in the peripheral blood and target organs were collected periodically from the GVHD hosts for analysis of chimerism formation and immune kinetics along the GVHD development via flow cytometry. Myeloid cells were tested for production of IL-17 via flow cytometry. Results: Pre-conditioning of BALB.B hosts with 900 cGy and 400 cGy resulted in different chimerism of leukocytes from the blood and affected survival of GVHD hosts. Profiles of leukocytes infiltrating GVHD target organs, rather than profiles of peripheral blood leukocytes (PBLs), were significantly influenced by irradiation dose. Proportions of IL-17 producing cells in the infiltrating $Gr-1^+$ or $Mac-1^+$ cells were higher in the GVHD hosts with high does irradiation than those with low dose irradiation. Conclusion: Pre-conditioning dose affected tissue infiltration of leukocytes and cytokine production by myeloid cells in the target organs.

• Clinical and Experimental Pediatrics
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• 제51권10호
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• pp.1112-1117
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• 2008

목 적: 해마 절편 배양에서 산소-포도당 박탈(oxygen-glucose deprivation, OGD)에 의한 세포 사망과 신경 세포 사멸을 propidium iodide(PI) 섭취, Fluoro-Jade(FJ) 염색, TUNEL 염색, caspase-3 면역형광염색 방법으로 관찰하고자 하였다. 방 법: 생후 7일된 Sprague-Dawley 흰쥐의 해마를 MacIlwain chopper로 $350{\mu}m$ 두께의 절편으로 절단하였다. 해마 절편을 6-well plate의 insert 내의 반 유공(sem-porous) 막 위에서 membrane-interface technique으로 10일 동안 배양하였다. 배양된 해마 절편에 산소-포도당 박탈을 60분 동안 가한 후 재산소-재관류하에 기초 배양액에서 48시간 배양하였다. 재산소-재관류 동안 PI 섭취 형광 정도를 시간에 따라 형광 현미경으로 관찰하고 세포사망 백분율(percent cell death)을 측정하였다. 산소-포도당 박탈 직전과 24 시간 후에 해마 절편을 $15{\mu}m$ 두께로 냉동 절단 후 FJ 염색, TUNEL 염색, caspase-3 면역형광염색을 시행하여 세포 사망을 관찰하였다. 결과: OGD 후 PI 섭취 는 해마 절편의 CA1과 DG에 한정되어있었다. OGD 후 재산소-재관류 동안 6시간에서 48시간까지 PI 섭취 형광 강도는 시간이 증가함에 따라 증가하였다. 세포 사망 백분율은 CA1과 DG에서 모두 OGD 후 재산소-재관류 시간이 증가함에 따라 의미 있게 증가하였다(P<0.05). OGD 후 24시간에 세포 변성을 의미하는 많은 FJ 염색 양성 신경 세포 들이 CA1과 DG에서 관찰되었다. 고배율 confocal laser 현미경으로 관찰한 CA1에서의 신경 세포들 중 일부는 명확한 핵과 돌기를 가지고 있는 것을 보여 주었으며, 다른 신경 세포들은 핵의 분절화, 돌기의 손실 등을 보여 주었다. TUNEL 염색과 caspase-3 염색은 OGD 후 24시간에 CA1과 DA에서 TUNEL 양성 발현을 증가시키고 caspase-3 발현을 증가시켰다. 결 론: 해마 절편 배양에서 산소-포도당 박탈 에 의한 다수의 세포 사망을 관찰할 수 있었다. 사망한 세포 들은 주로 신경 세포의 caspase-3 활성화에 의해 매개된 사멸을 보였다.

• Asian-Australasian Journal of Animal Sciences
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• 제27권7호
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• pp.1013-1018
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• 2014

In this study, we developed kinetic models to predict the growth of pathogenic Escherichia coli on cheeses during storage at constant and changing temperatures. A five-strain mixture of pathogenic E. coli was inoculated onto natural cheeses (Brie and Camembert) and processed cheeses (sliced Mozzarella and sliced Cheddar) at 3 to 4 log CFU/g. The inoculated cheeses were stored at 4, 10, 15, 25, and $30^{\circ}C$ for 1 to 320 h, with a different storage time being used for each temperature. Total bacteria and E. coli cells were enumerated on tryptic soy agar and MacConkey sorbitol agar, respectively. E. coli growth data were fitted to the Baranyi model to calculate the maximum specific growth rate (${\mu}_{max}$; log CFU/g/h), lag phase duration (LPD; h), lower asymptote (log CFU/g), and upper asymptote (log CFU/g). The kinetic parameters were then analyzed as a function of storage temperature, using the square root model, polynomial equation, and linear equation. A dynamic model was also developed for varying temperature. The model performance was evaluated against observed data, and the root mean square error (RMSE) was calculated. At $4^{\circ}C$, E. coli cell growth was not observed on any cheese. However, E. coli growth was observed at $10{\circ}C$ to $30^{\circ}C$C with a ${\mu}_{max}$ of 0.01 to 1.03 log CFU/g/h, depending on the cheese. The ${\mu}_{max}$ values increased as temperature increased, while LPD values decreased, and ${\mu}_{max}$ and LPD values were different among the four types of cheese. The developed models showed adequate performance (RMSE = 0.176-0.337), indicating that these models should be useful for describing the growth kinetics of E. coli on various cheeses.

• 대한전자공학회논문지TC
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• 제42권8호
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• pp.11-16
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• 2005

본 논문은 스크램블링(Scrambling), 길쌈부호화(Convolutional Encoding), 펑처링(Puncturing), 인터리빙(Interleaving) 등과 같은 연산에 공통적으로 필요한 비트 조작(Bit Manipulation)을 효율적으로 지원하기 위한 비트 조작 연산 가속기를 제안한다. 기존의 DSP는 곱셈 및 가산 연산을 기본으로 연산기가 구성되어 있으며 워드 단위로 동작을 함으로 비트 조작 연산의 경우 비효율적인 연산을 수행할 수밖에 없다. 그러나 제안한 가속기는 비트 조작 연산을 다수의 데이터에 대해 병렬 쉬프트와 XOR 연산, 비트 추출 및 삽입 연산을 효율적으로 수행할 수 있다. 제안한 가속기는 VHDL로 구현 하여 삼성 $0.18\mu m$ 표준 셀 라이브러리를 이용하여 합성하였으며 가속기의 게이트 수는 1,700개에 불과하다. 제안한 가속기를 통해 스크램블링, 길쌈부호화, 인터리빙을 수행시 기존의 DSP에 비해 $40\~80\%$의 연산 사이클의 절감이 가능하였다.

• ETRI Journal
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• 제25권5호
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• pp.337-344
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• 2003

In this paper, we introduce a fully synthesizable 32-bit embedded microprocessor core called the AE32000B. The AE32000B core is based on the extendable instruction set computer architecture, so it has high code density and a low memory access rate. In order to improve the performance of the core, we developed and adopted various design options, including the load extension register instruction (LERI) folding unit, a high performance multiply and accumulate (MAC) unit, various DSP units, and an efficient coprocessor interface. The instructions per cycle count of the Dhrystone 2.1 benchmark for the designed core is about 0.86. We verified the synthesizability and the area and time performances of our design using two CMOS standard cell libraries: a 0.35-${\mu}m$ library and a 0.18-${\mu}m$ library. With the 0.35-${\mu}m$ library, the core can be synthesized with about 47,000 gates and operate at 70 MHz or higher, while it can be synthesized with about 53,000 gates and operate at 120 MHz or higher with the 0.18-${\mu}m$ library.

• Journal of Ship and Ocean Technology
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• 제12권1호
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• pp.16-27
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• 2008

The interaction between advancing ships and the waves generated by them plays important roles in wave resistances and ship motions. Wave breaking phenomena near the ship bow at different speeds are investigated both numerically and experimentally. Numerical simulations of free surface profiles near the fore bodies of ships are performed and visualized to grasp the general trend or the mechanism of wave breaking phenomena from moderate waves rather than concentrating on local chaotic irregularities as ship speeds increase. Navier-Stokes equations are differentiated based on the finite difference method. The Marker and Cell (MAC) Method and Marker-Density Method are employed, and they are compared for the description of free surface conditions associated with the governing equations. Extra effort has been directed toward the realization of extremely complex free surface conditions at wave breaking. For this purpose, the air-water interface is treated with marker density, which is used for two layer flows of fluids with different properties. Adaptation schemes and refinement of the numerical grid system are also used at local complex flows to improve the accuracy of the solutions. In addition to numerical simulations, various model tests are performed in a ship model towing tank. The results are compared with numerical calculations for verification and for realizing better, more efficient research performance. It is expected that the present research results regarding wave breaking and the geometry of the fore body of ship will facilitate better hull form design productivity at the preliminary ship design stage, especially in the case of small and fast ship design. Also, the obtained knowledge on the impact due to the interaction of breaking waves and an advancing hull surface is expected to be applicable to investigation of the ship bow slamming problem as a specific application.

• Journal of Radiation Protection and Research
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• 제42권4호
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• pp.177-188
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• 2017

Background: Radiation-induced pneumonitis and pulmonary fibrosis are common dose-limiting complications in patients receiving radiotherapy for lung, breast, and lymphoid cancers. In this study, we investigated the characteristics of effective immune cells related to pneumonitis and fibrosis after irradiation. Materials and Methods: After anesthesia, the whole thorax of C57BL/6 mice was irradiated at 14 Gy. The lung tissue and bronchoalveolar lavage fluid were collected at defined time points post-irradiation for the determination of histological and immunohistochemical analysis and inflammatory cell population infiltrated into the lung. Results and Discussion: Whole thoracic irradiation increased the deposition of extracellular matrix (ECM), lung weight, and pleural effusions, which started to die from 4 months later. At 4 months after irradiation, the numbers of macrophages and lymphocytes as well as neutrophils were increased dramatically in the lung. Interestingly, the macrophages that were recruited into the lung after irradiation had an enlarged foamy morphology. In addition, the expressions of chemokines (CCL-2, CCL-3, CXCL-10) for the attraction of macrophages and T cells were higher in the lung of irradiated mice. The high expressions of these chemokines were sustained up to 6 months following irradiation. In thoracic irradiated mice, infiltrated macrophages into the lung had the high levels of Mac-3 antigens on their surface and upregulated the hallmarks of alternatively activated macrophages such as arginase-1 and CD206. Furthermore, the levels of IL-4 and IL-13 were higher in a BAL fluid of irradiated mice. Conclusion: All results show that thoracic irradiation induces to infiltrate various inflammation-related immune cells, especially alternatively activated macrophages, through enhancing the expression of chemokines, suggesting that alternatively activated macrophages are most likely important for leading to pulmonary fibrosis.