Image-to-Image Translation with GAN for Synthetic Data Augmentation in Plant Disease Datasets

Nazki, Haseeb,Lee, Jaehwan,Yoon, Sook,Park, Dong Sun THE KOREAN INSTITUTE OF SMART MEDIA 2019 스마트미디어저널 Vol.8 No.2

In recent research, deep learning-based methods have achieved state-of-the-art performance in various computer vision tasks. However, these methods are commonly supervised, and require huge amounts of annotated data to train. Acquisition of data demands an additional costly effort, particularly for the tasks where it becomes challenging to obtain large amounts of data considering the time constraints and the requirement of professional human diligence. In this paper, we present a data level synthetic sampling solution to learn from small and imbalanced data sets using Generative Adversarial Networks (GANs). The reason for using GANs are the challenges posed in various fields to manage with the small datasets and fluctuating amounts of samples per class. As a result, we present an approach that can improve learning with respect to data distributions, reducing the partiality introduced by class imbalance and hence shifting the classification decision boundary towards more accurate results. Our novel method is demonstrated on a small dataset of 2789 tomato plant disease images, highly corrupted with class imbalance in 9 disease categories. Moreover, we evaluate our results in terms of different metrics and compare the quality of these results for distinct classes.

Image-to-Image Translation with GAN for Synthetic Data Augmentation in Plant Disease Datasets

Haseeb Nazki,Jaehwan Lee,Sook Yoon,Dong Sun Park 한국스마트미디어학회 2019 스마트미디어저널 Vol.8 No.2

In recent research, deep learning-based methods have achieved state-of-the-art performance in various computer vision tasks. However, these methods are commonly supervised, and require huge amounts of annotated data to train. Acquisition of data is an additional costly effort, particularly for the tasks where it becomes challenging to obtain large amounts of data considering the time constraints and the requirement of professional human diligence. In this paper, we present a data level synthetic sampling solution to learn from small and imbalanced data sets using Generative Adversarial Networks (GANs). The reason for using GANs are the challenges posed in various fields to manage with the small datasets and fluctuating amounts of samples per class. As a result, we present an approach that can improve learning with respect to data distributions, reducing the partiality introduced by class imbalance and hence shifting the classification decision boundary towards more accurate results. Our novel method is demonstrated on a small dataset of 2789 tomato plant disease images, highly corrupted with class imbalance in 9 disease categories. Moreover, we evaluate our results in terms of different metrics and compare the quality of these results for distinct classes.

Synthetic Data Augmentation for Plant Disease Image Generation using GAN

Haseeb Nazki(나즈키 하십),Jaehwan Lee(이재환),Sook Yoon(윤숙),Dong Sun Park(박동선) 한국콘텐츠학회 2018 한국콘텐츠학회 종합학술대회 논문집 Vol.2018 No.5

Assessment of the replication efficiency of porcine reproductive and respiratory syndrome viruses (PRRSVs) in porcine alveolar macrophages (PAMs) at different age of host-pigs

Amina Khatun,Salik Nazki,A Rum Kang,Chang Gi Jeong,Jhung hyun Juhng,Byoung Joo Seo,Won Il Kim 대한수의학회 2016 대한수의학회 학술대회발표집 Vol.2016 No.-

PRRS 저항성 유전형 자돈의 생산 및 평가

정창기,Amina Khatun,Salik Nazki,이심인,김태헌,김관석,박최규,김원일 한국동물위생학회 2019 韓國家畜衛生學會誌 Vol.42 No.1

Porcine reproductive and respiratory syndrome (PRRS) is economically the most important and challeng-ing disease in swine industries worldwide and caused by PRRS virus (PRRSV). Previous studies re-ported that pigs with heterozygous genotypes in the guanylate-binding proteins (GBP1 and GBP5) ex-hibited increased resistance against PRRSV infection. The present study was conducted to produce high-er numbers of the heterozygous pigs based on the PRRS resistant polymorphisms found in GBP1 (GBP1E2 and WUR) and GBP5, and evaluate the resistance of heterozygous pigs against challenge with a type 2 PRRSV (JA142) in comparison with homozygous pigs. In the challenge study, 12, 4 week-old PRRSV-negative piglets were selected based on the genotypes of the 3 polymorphisms (GBP1E2, WUR and GBP5). Among them, 8 piglets [homozygous (n=4) and heterozygous (n=4)] were challenged with JA142 and kept in the same room, and the remaining 4 piglets were kept separately as a negative control. In results, the sperms collected from the boars of GBP1E2-GG genotype produced approx-imately 28∼41% higher numbers of heterozygous piglets as compared with those from the boars of GBP1E2-AG genotype. In the challenge study, we found that heterozygous piglets showed the sig-nificantly lower levels of viremia than homozygous piglets at 14, 21 and 28 dpc. Consistently, these heterozygous piglets also exhibited significantly higher ADWG than homozygous piglets. Therefore, in the current study, selection of boars based on SNP markers could increase the production of PRRS re-sistant piglets and the PRRS resistant pigs were found to be more resistant to PRRSV infection.

Plant synthetic GP4 and GP5 proteins from porcine reproductive and respiratory syndrome virus elicit immune responses in pigs

An, Chul Han,Nazki, Salik,Park, Sung-Chul,Jeong, Yu Jeong,Lee, Ju Huck,Park, Su-Jin,Khatun, Amina,Kim, Won-Il,Park, Youn-Il,Jeong, Jae Cheol,Kim, Cha Young Springer-Verlag 2018 Planta Vol.247 No.4

<P>Porcine reproductive and respiratory syndrome virus (PRRSV) causes PRRS, the most economically significant disease affecting the swine industry worldwide. However, current commercial PRRSV vaccines (killed virus or modified live vaccines) show poor efficacy and safety due to concerns such as reversion of virus to wild type and lack of cross protection. To overcome these problems, plants are considered a promising alternative to conventional platforms and as a vehicle for large-scale production of recombinant proteins. Here, we demonstrate successful production of recombinant protein vaccine by expressing codon-optimized and transmembrane-deleted recombinant glycoproteins (GP4D and GP5D) from PRRSV in planta. We generated transgenic Arabidopsis plants expressing GP4D and GP5D proteins as candidate antigens. To examine immunogenicity, pigs were fed transgenic Arabidopsis leaves expressing the GP4D and GP5D antigens (three times at 2-week intervals) and then challenged with PRRSV at 6-week post-initial treatment. Immunized pigs showed significantly lower lung lesion scores and reduced viremia and viral loads in the lung than pigs fed Arabidopsis leaves expressing mYFP (control). Immunized pigs also had higher titers of PRRSV-specific antibodies and significantly higher levels of pro-inflammatory cytokines (TNF-alpha and IL-12). Furthermore, the numbers of IFN-gamma(+)-producing cells were higher, and those of regulatory T cells were lower, in GP4D and GP5D immunized pigs than in control pigs. Thus, plant-derived GP4D and GP5D proteins provide an alternative platform for producing an effective subunit vaccine against PRRSV.</P>

Comparison of immune cell populations in bronchoalveolar lavage cells and PBMC cytokine expressions in porcine reproductive and respiratory syndrome and porcine respiratory disease complex

Yang, Myeon-Sik,Jeong, Chang-Gi,Nazki, Salik,Mattoo, Sameer ul Salam,Lee, Sang-Myeong,Kim, Won-Il,Kim, Bumseok The Korean Society of Veterinary Service 2019 韓國家畜衛生學會誌 Vol.42 No.4

Porcine reproductive and respiratory syndrome (PRRS) is characterized by reproductive failure in sows and respiratory distress in all age pigs. Porcine respiratory disease complex (PRDC) is a disease caused by opportunistic bacterial infection secondary to a weakened immune system by a preceding respiratory infection. In this study, we tried to compare the immune responses in PRRS and PRDC groups to clearly characterize the disease severity. Eighty-five pigs were infected with various Korean field PRRS virus strains. Infected animals were classified into PRRS (n=32) and PRDC (n=53) groups based on lung lesions such as interstitial pneumonia, suppurative pneumonia, and pleuropneumonia. The immune cell population of bronchoalveolar lavage cells (BALc) was evaluated on 14 and 28 days post infection (dpi) and PMBC cytokine expression was measured on 0, 3, 7, 14 dpi to investigate early inflammatory reactions. Pulmonary lesion severity was negatively correlated with alveolar macrophage (AM) in both PRRS and PRDC groups on 14 and 28 dpi. AM in BALc was less populated in PRDC group on 28 dpi compared to PRRS group. AM in BALc was significantly less populated in PRDC group on 28 dpi compared to 14 dpi. In addition, cytotoxic T lymphocyte (CTL) in BALc was higher populated in PRDC group on 14 dpi and 28 dpi compared to PRRS group. In the case of PBMC cytokine TNF-α, IFN-α, IL-1β, IFN-γ, FoxP3, and IL-2, the PRRS group showed higher expression than the PRDC group on 7 dpi, 14 dpi, 7 dpi, 14 dpi, 14 dpi, and 14 dpi, respectively. On the other hand, in the case of IFN-β, IL-6, IL-8, IL-4, and IL-17, the PRDC group showed higher PBMC cytokine expression at 14 dpi, 7 dpi, 14 dpi, 3 dpi, and 3 dpi, respectively, than the PRRS group. Based on these results, our study could characterize differential immune responses in pigs with PRRS or PRDC.

Evaluation of different media for ex vivo porcine lung culture model

Yang, Myeon-Sik,Zhou, Zixiong,Khatun, Amina,Nazki, Salik,Jeong, Chang Gi,Kim, Won Il,Lee, Sang Myeong,Kang, Seog-Jin,Lim, Chae Woong,Kim, Bumseok The Korean Society of Veterinary Service 2018 韓國家畜衛生學會誌 Vol.41 No.4

Developing drugs targeting respiratory pathogen is essential to control respiratory diseases. Many experiments have been performed under in vivo situation. However, in vivo experiments have economical and ethical issues. The objective of this study was to determine the possibility of developing an ex vivo lung culture system with possible application for respiratory infection studies. After isolating lungs from naïve pigs, agarose-inflated lung tissues were prepared and sliced manually. These sliced lung tissues were then subsequently placed on 24-well plates. Eight different combinations of media were used to determine the optimum ex vivo lung culture condition. In addition, lung tissues were infected with porcine reproductive and respiratory syndrome (PRRS) virus at a titer of $1{\times}10^4\;TCID_{50}/mL$. Virus growth was confirmed by titration in MARC-145 cells at 2, 4, 6 days post infection (dpi). We found that ex vivo lung culture in physiological environment was not media specific based on histopathology and cytotoxicity. However, under virus-infected condition, thickened alveolar walls in the lung tissues and stable virus titers at 2, 4, 6 dpi were shown in F12K medium suggesting that it was useful for tissue maintenance and virus infection using PRRS virus infected lung tissues. The present study shows the possibility of using porcine ex vivo lung model for respiratory infection studies.

Comparison of immune cell populations in bronchoalveolar lavage cells and PBMC cytokine expressions in porcine reproductive and respiratory syndrome and porcine respiratory disease complex

Myeon-Sik Yang,정창기,Salik Nazki,Sameer ul Salam Mattoo,Sang-Myeong Lee,Won-Il Kim,Bumseok Kim 한국동물위생학회 2019 韓國家畜衛生學會誌 Vol.42 No.4

Porcine reproductive and respiratory syndrome (PRRS) is characterized by reproductive failure in sows and respiratory distress in all age pigs. Porcine respiratory disease complex (PRDC) is a disease caused by opportunistic bacterial infection secondary to a weakened immune system by a preceding respiratory infection. In this study, we tried to compare the immune responses in PRRS and PRDC groups to clearly characterize the disease severity. Eighty-five pigs were infected with various Korean field PRRS virus strains. Infected animals were classified into PRRS (n=32) and PRDC (n=53) groups based on lung le-sions such as interstitial pneumonia, suppurative pneumonia, and pleuropneumonia. The immune cell population of bronchoalveolar lavage cells (BALc) was evaluated on 14 and 28 days post infection (dpi) and PMBC cytokine expression was measured on 0, 3, 7, 14 dpi to investigate early inflammatory re-actions. Pulmonary lesion severity was negatively correlated with alveolar macrophage (AM) in both PRRS and PRDC groups on 14 and 28 dpi. AM in BALc was less populated in PRDC group on 28 dpi compared to PRRS group. AM in BALc was significantly less populated in PRDC group on 28 dpi compared to 14 dpi. In addition, cytotoxic T lymphocyte (CTL) in BALc was higher populated in PRDC group on 14 dpi and 28 dpi compared to PRRS group. In the case of PBMC cytokine TNF-, IFN-, IL-1, IFN-, FoxP3, and IL-2, the PRRS group showed higher expression than the PRDC group on 7 dpi, 14 dpi, 7 dpi, 14 dpi, 14 dpi, and 14 dpi, respectively. On the other hand, in the case of IFN-, IL-6, IL-8, IL-4, and IL-17, the PRDC group showed higher PBMC cytokine expression at 14 dpi, 7 dpi, 14 dpi, 3 dpi, and 3 dpi, respectively, than the PRRS group. Based on these results, our study could characterize differential immune responses in pigs with PRRS or PRDC.

Evaluation of different media for ex vivo porcine lung culture model

Myeon-Sik Yang,Zixiong Zhou,Amina Khatun,Salik Nazki,정창기,김원일,이상명,Seog-Jin Kang,임채웅,김범석 한국동물위생학회 2018 韓國家畜衛生學會誌 Vol.41 No.4

Developing drugs targeting respiratory pathogen is essential to control respiratory diseases. Many experi-ments have been performed under in vivo situation. However, in vivo experiments have economical and ethical issues. The objective of this study was to determine the possibility of developing an ex vivo lung culture system with possible application for respiratory infection studies. After isolating lungs from naïve pigs, agarose-inflated lung tissues were prepared and sliced manually. These sliced lung tissues were then subsequently placed on 24-well plates. Eight different combinations of media were used to determine the optimum ex vivo lung culture condition. In addition, lung tissues were infected with por-cine reproductive and respiratory syndrome (PRRS) virus at a titer of 1×104 TCID50/mL. Virus growth was confirmed by titration in MARC-145 cells at 2, 4, 6 days post infection (dpi). We found that ex vivo lung culture in physiological environment was not media specific based on histopathology and cytotoxicity. However, under virus-infected condition, thickened alveolar walls in the lung tissues and stable virus titers at 2, 4, 6 dpi were shown in F12K medium suggesting that it was useful for tissue maintenance and virus infection using PRRS virus infected lung tissues. The present study shows the possibility of using porcine ex vivo lung model for respiratory infection studies.