지문 영상 잡음 제거 및 복원을 위한 심층 합성곱 신경망

학위논문 (석사) -- 서울대학교 대학원 : 자연과학대학 협동과정 계산과학전공, 2021. 2. 강명주.Biometric authentication using fingerprints requires a method for image denoising and inpainting to extract fingerprints from degraded fingerprint images. A few deep learning models for fingerprint image denoising and inpainting were proposed in ChaLearn LAP Inpainting Competition - Track 3, ECCV 2018. In this thesis, a new deep learning model for fingerprint image denoising is proposed. The proposed model is adapted from FusionNet, which is a convolutional neural network based deep learning model for image segmentation. The performance of the proposed model was demonstrated using the dataset from the ECCV 2018 ChaLearn Competition. It was shown that the proposed model obtains better results compared with the models that achieved high performances in the competition.지문을 사용한 생체 인식 인증은 품질이 저하된 지문 영상에서 지문을 추출하기 위한 영상 잡음 제거 및 복원 방법을 필요로 한다. 지문 영상 잡음 제거 및 복원을 위한 몇 가지 딥러닝 모델이 ChaLearn LAP Inpainting Competition - Track 3, ECCV 2018에서 제안되었다. 본 논문에서는 지문 영상 잡음 제거를 위한 새로운 딥러닝 모델을 제안한다. 제안된 모델은 영상 분할을 위한 합성곱 신경망 기반 딥러닝 모델인 FusionNet을 수정하여 작성하였다. 제안된 모델의 성능은 ChaLearn Competition의 데이터셋을 사용하여 검증되었다. 이를 통해 제안된 모델이 대회에서 높은 성능을 획득한 다른 모델들에 비하여 더 나은 결과를 얻음을 확인하였다.Abstract i Contents ii 1 Introduction 1 2 Related Work 3 2.1 Residual Neural Network . . . . . . . . . . . . . . . . . . . . . . . . 3 2.2 Convolutional Neural Networks for Semantic Segmentation . . . . . . 4 2.2.1 U-Net . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2.2.2 FusionNet . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2.3 Recent Trends in Fingerprint Image Denoising . . . . . . . . . . . . . 6 3 Proposed Model 7 3.1 Model Architecture . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 3.2 Architecture Detail . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 3.2.1 Residual Block . . . . . . . . . . . . . . . . . . . . . . . . . 9 3.2.2 Encoder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 3.2.3 Bridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 3.2.4 Decoder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 3.3 Loss Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 4 Experiments 13 4.1 Experimental Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 4.2 Evaluation Metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 4.3 Dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 4.4 Experimental Results . . . . . . . . . . . . . . . . . . . . . . . . . . 16 4.4.1 Ablation Study . . . . . . . . . . . . . . . . . . . . . . . . . 16 4.4.2 Comparison with Other Models . . . . . . . . . . . . . . . . 17 5 Conclusion 21 Abstract (In Korean)Maste

Paip1 Indicated Poor Prognosis in Cervical Cancer and Promoted Cervical Carcinogenesis

PURPOSE: This study was aimed to investigate the role of poly(A)-binding protein-interacting protein 1 (Paip1) in cervical carcinogenesis. Materials and Methods: The expression of Paip1 in normal cervical epithelial tissues and cervical cancer (CC) tissues were detected by immunohistochemistry. In vivo and in vitro assays were performed to validate effect of Paip1 on CC progression. RESULTS: Paip1 was found to be up-regulated in CC, which was linked with shorter survival. Knockdown of Paip1 inhibited cell growth, induced apoptosis and cell cycle arrest in CC cells, whereas its overexpression reversed these effects. The in vivo tumor model confirmed the pro-tumor role of Paip1 in CC growth. CONCLUSION: Altogether, the investigation demonstrated the clinical significance of Paip1 expression, which prompted that the up-regulated of Paip1 can presumably be a potential prognostic and progression marker for CC.ope

Inflammatory Cytokines and Oral Squamous Cell Carcinoma

Inflammation functions as a double-edged sword against external stimulus. For instance, inflammation can have anti-cancer effect and simultaneously can play cancer-promoting factors. Recent studies have shown that cytokine plays an important role in tumor biology by influencing tumor growth, invasion and metastasis. We classify these cytokines by cancer type and review current knowledge of cytokines in terms of carcinogenesis. Here, we also focus on whether cytokines can act as biomarkers for early detection of oral squamous cell carcinoma (OSCC). This review will provide basis for further approach to study the role of cytokines in carcinogenesis and evaluating the possibilities of cytokines as biomarkers for cancer detection.ope

Biochemical and Histological Evaluations of Articular Cartilages Preserved in Cold Storage Solution Containing Green Tea Catechin, EGCG

Although epigallocatechin-3-O-gallate(EGCG), a major poly phenolic constituent of green tea, has various pharmacological and biological activities including anti-carcinogenic, anti-thrombotic and anti-inflammatory effects, relatively a little is known about its beneficial effects on the non-frozen preservation of mammalian cells and tissues. In this study, articular cartilages from human knee joint were pretreated with 1 mM EGCG for 1 d and then preserved in serum-free RPMI 1640 media with 1% antibiotic-antimycotic solution at 4oC for 1, 2 and 4 wk. After cold preservation, chondrocyte viability(CCK-8 assay), biochemical and immunohistochemical composition[glycosaminoglycans and(type II)collagen], and biomechanical property(compressive elastic modulus) were assessed, respectively. Chondrocyte viability of cartilages pretreated with EGCG was significantly well-maintained for at least 2 wk with high contents of glycosaminoglycan and total collagen. These beneficial effects of EGCG pretreatment were more confirmed by histological and immunohistochemical observations showing well-preserved cartilaginous structures and delayed denaturation of the extracellular matrices in preserved specimens. The compressive elastic modulus(MPa) of cartilages pretreated with EGCG was well-maintained as much as that of fresh specimens without any increase as the progress in the preservation period. Here were also found that fluorescein isothiocyanate-conjugated EGCG were widely distributed through the matrix and clearly observed at the chondrocytes in the lacunas. Taking these results into consideration, it is suggested that EGCG may play an effective role in preserving articular cartilages, which be exploited to craft strategies for the long-term preservation of osteochondral allografts under cold storage conditions.ope

Reciprocal interaction between carcinoma-associated fibroblasts and squamous carcinoma cells through interleukin-1α induces cancer progression.

Crosstalk between cancer cells and carcinoma-associated fibroblasts (CAFs) has earned recognition as an interaction that plays a pivotal role in carcinogenesis. Thus, we attempted to clarify whether increase in the level of CAFs promotes cancer progression by proportionally enhancing the interaction between cancer cells and CAFs. We first analyzed clinical correlation between the levels of fibroblasts and cancer progression and found that the level of CAFs made a noticeable difference on the prognosis of patients with oral squamous cell carcinoma (OSCC). In vivo animal study also demonstrated that tumor volume depended on the dose of CAFs that was co-injected with OSCC cells. The same tendency was observed in an in vitro study. We also found that interleukin-1α (IL-1α) secreted from OSCC cells had dual effects on CAFs: IL-1α not only promoted the proliferation of CAFs but also upregulated the secretion of cytokines in CAFs such as CCL7, CXCL1, and IL-8. The induction activity of cytokine secretion by IL-1α surpassed that of proliferation in OSCC cells. In summary, we unraveled an important interactive mechanism of carcinogenesis: IL-1α released from carcinoma stimulates the proliferation of CAFs and the simultaneous increase in cytokine secretion from CAFs promotes cancer progression in human OSCC. On the basis of these findings, we propose that the level of CAFs is eligible for being selected as a prognostic factor that will be useful in routine diagnosis. We also propose that blockage of reciprocal interaction between cancer cells and CAFs will provide an insight for developing novel chemotherapeutic strategy.ope

SpCas9 activity prediction by DeepSpCas9, a deep learning-based model with high generalization performance

We evaluated SpCas9 activities at 12,832 target sequences using a high-throughput approach based on a human cell library containing single-guide RNA-encoding and target sequence pairs. Deep learning-based training on this large dataset of SpCas9-induced indel frequencies led to the development of a SpCas9 activity-predicting model named DeepSpCas9. When tested against independently generated datasets (our own and those published by other groups), DeepSpCas9 showed high generalization performance. DeepSpCas9 is available at http://deepcrispr.info/DeepSpCas9.ope

Human telomerase reverse transcriptase (hTERT) promotes cancer invasion by modulating cathepsin D via early growth response (EGR)-1

Human telomerase reverse transcriptase (hTERT) contributes to tumor progression as well as maintaining telomere length, however, the mechanism by which hTERT promotes invasiveness is not yet completely understood. This study aims to unravel the precise mechanism through which hTERT promotes cancer invasion. We established an hTERT-overexpressed immortalized cell line (IHOK/hTERT). In orthotopic xenograft models, IHOK/hTERT harbors higher tumorigenicity than IHOK/Control. IHOK/hTERT showed much higher migration and invasion activities compared to IHOK/Control. IHOK/hTERT co-cultured with fibroblasts displayed increased invasion compared to IHOK/hTERT without fibroblasts. We screened for genes that play an important role in intermodulation between cancer cells and fibroblasts using a microarray and identified fibroblast activation protein (FAP). hTERT knockdown showed decreased expression of FAP and early growth response (EGR)-1, one of the transcriptional regulators of FAP in IHOK/hTERT and oral cancer cell line YD10B. Furthermore, EGR-1 knockdown in IHOK/hTERT and YD10B showed reduced invasion and reduced cathepsin D expression compared to Control-siRNA cells. Taken together, this study provides evidence that hTERT overexpression is responsible for the upregulation of the cysteine protease cathepsin D by regulating EGR-1 to activate invasiveness in cancer progression.ope

RUNX3 confers sensitivity to pheophorbide a-photodynamic therapy in human oral squamous cell carcinoma cell lines

Photodynamic therapy (PDT) with photosensitizer is one of the promising modalities for cancer treatment. For clinical use of PDT, screening process should be preceded to enhance sensitivity to PDT. Thus, we investigated a molecular biomarker to determine the sensitivity to pheophorbide a (Pa)-PDT in immortalized human oral keratinocytes (IHOK) and oral squamous cell carcinoma (OSCC) cell lines. Two IHOK and several OSCC cell lines were used. After Pa-PDT, cell viability was reduced by more than 50%, and reactive oxygen species were generated in IHOK and OSCC cell lines. Additionally, apoptosis occurred in PDT-treated cells. IHOK(S) and IHOK(P), the two IHOK cell lines derived from the same source, showed a difference in cytotoxicity after Pa-PDT. To explain this difference in cytotoxicity, we looked at the expression of Wnt signaling-related genes in these two cell lines, for the morphology of IHOK(S) which was spindle like and elongated and distinct from IHOK(P) and the parent cell. Among the relevant genes, runt-related transcription factor 3 (RUNX3), an apoptosis-related gene, was selected as a potential marker that confers sensitivity to PDT. We found that the cytotoxicity by Pa-PDT was proportional to RUNX3 expression in OSCC cell lines. Additionally, knockdown of RUNX3 expression reduced cytotoxicity by Pa-PDT, suggesting that RUNX3 might be a biomarker to determine sensitivity to Pa-PDT. This was the first study to find a new target molecule that enhances Pa-PDT effects in IHOK and OSCC cell lines. Hence, the development of a PDT-dependent biomarker could provide a novel approach to improve the effects of PDT on oral precancerous and cancerous lesions.ope

A distinct role for interleukin-6 as a major mediator of cellular adjustment to an altered culture condition

Tissue microenvironment adjusts biological properties of different cells by modulating signaling pathways and cell to cell interactions. This study showed that epithelial-mesenchymal transition (EMT)/ mesenchymal-epithelial transition (MET) can be modulated by altering culture conditions. HPV E6/E7-transfected immortalized oral keratinocytes (IHOK) cultured in different media displayed reversible EMT/MET accompanied by changes in cell phenotype, proliferation, gene expression at transcriptional, and translational level, and migratory and invasive activities. Cholera toxin, a major supplement to culture medium, was responsible for inducing the morphological and biological changes of IHOK. Cholera toxin per se induced EMT by triggering the secretion of interleukin 6 (IL-6) from IHOK. We found IL-6 to be a central molecule that modulates the reversibility of EMT based not only on the mRNA level but also on the level of secretion. Taken together, our results demonstrate that IL-6, a cytokine whose transcription is activated by alterations in culture conditions, is a key molecule for regulating reversible EMT/MET. This study will contribute to understand one way of cellular adjustment for surviving in unfamiliar conditions.ope

Effective vitrification of human induced pluripotent stem cells using carboxylated ε-poly-l-lysine

Derivation of human induced pluripotent stem (iPS) cells could enable their widespread application in future. Establishment of highly efficient and reliable methods for their preservation is a prerequisite for these applications. In this study, we developed a vitrification solution comprising ethylene glycol (EG) and sucrose as well as carboxylated ε-poly-l-lysine (PLL); this solution inhibited devitrification. Human iPS cells were vitrified in 200-μL vitrification solutions comprised 6.5M EG, 0.75 M sucrose and 0 or 10%w/v carboxylated PLL with 65 mol% of the amino groups converted to carboxyl groups [PLL (0.65)] in a cryovial by directly immersing in liquid nitrogen. After warming, attached colony and recovery rates of human iPS cells vitrified by adding PLL (0.65) were significantly higher than those for cells without PLL (0.65) and vitrification solution (DAP213: 2M dimethyl sulfoxide, 1M acetamide and 3M propylene glycol). Furthermore, even after warming at room temperature, attached colony and recovery rates of iPS cells vitrified with PLL (0.65) were reduced to a lesser extent than those vitrified with either DAP213 or EG and sucrose without PLL (0.65). This could be attributed to inhibition of devitrification by PLL (0.65), as differential scanning calorimetry indicated less damage after vitrification with PLL (0.65). In addition, human iPS cells vitrified in the solution with PLL (0.65) had normal karyotypes and maintained undifferentiated states and pluripotency as determined by immunohistochemistry and teratoma formation. Addition of PLL (0.65) successfully vitrified human iPS cells with high efficiency. We believe that this method could aid future applications and increase utility of human iPS cells.ope