• Proceedings of the Korean Society for Applied Microbiology Conference
• /
• 2001.06a
• /
• pp.47-57
• /
• 2001

• KIISE Transactions on Computing Practices
• /
• v.22 no.1
• /
• pp.56-60
• /
• 2016

Peptide identification in tandem mass spectrometry is usually done by searching the spectra against target databases consisting of reference protein sequences. To control false discovery rates for high-confidence peptide identification, spectra are also searched against decoy databases constructed by permuting reference protein sequences. In this case, a peptide of the same sequence could be included in both the target and the decoy databases or multiple entries of a same peptide could exist in the decoy database. These phenomena make the protein identification problem complicated. Thus, it is important to minimize the number of such redundant peptides for accurate protein identification. In this regard, we examined two popular methods for decoy database generation: 'pseudo-shuffling' and 'pseudo-reversing'. We experimented with target databases of varying sizes and investigated the effect of the maximum number of missed cleavage sites allowed in a peptide (MC), which is one of the parameters for target and decoy database generation. In our experiments, the level of redundancy in decoy databases was proportional to the target database size and the value of MC, due to the increase in the number of short peptides (7 to 10 AA). Moreover, 'pseudo-reversing' always generated decoy databases with lower levels of redundancy compared to 'pseudo-shuffling'.

• Journal of the Korea Institute of Information Security & Cryptology
• /
• v.33 no.6
• /
• pp.919-928
• /
• 2023

Deep learning technology is used in various fields such as self-driving cars, image creation, and virtual voice implementation, and deep learning accelerators have been developed for high-speed operation in hardware devices. However, several side channel attacks that recover secret information inside the accelerator using side-channel information generated when the deep learning accelerator operates have been recently researched. In this paper, we implemented a DNN(Deep Neural Network)-based MNIST digit classifier on a microprocessor and attempted a correlation power analysis attack to confirm that the weights of deep learning accelerator could be sufficiently recovered. In addition, to counter these power analysis attacks, we proposed a Node-CUT shuffling method that applies the principle of misalignment at the time of power measurement. It was confirmed through experiments that the proposed countermeasure can effectively defend against side-channel attacks, and that the additional calculation amount is reduced by more than 1/3 compared to using the Fisher-Yates shuffling method.

• Korean Journal of Microbiology
• /
• v.48 no.2
• /
• pp.73-78
• /
• 2012

We previously reported that the truncated Cel44C-$Man26A_{P558}$ ${\beta}$-glycosyl hydrolase protein exhibits multifunctional activities, including cellulase, xylanase, and lichenase. DNA shuffling of the truncated Cel44C-$Man26A_{P558}$ enzyme was performed to enhance the enzymatic activity of the multifunctional ${\beta}$-glycosyl hydrolase. Two mutant enzymes, M2Cel44C-$Man26A_{P558}$ that carries one mutation (P438A) and M21Cel44C-$Man26A_{P558}$ that carries two mutations (A273T and P438A) were obtained. The enzymatic activity of the M21Cel44C-$Man26A_{P558}$ double mutant was lower than enzymatic activity of the single mutant (M2Cel44C-$Man26A_{P558}$). However, both mutants displayed the enhancements in their enzyme activities that were ${\approx}1.3$- to 2.2-fold higher than the original enzymatic activity in Cel44C-$Man26A_{P558}$. In particular, the mutant M2Cel44C-$Man26A_{P558}$ exhibited an approximate 1.5- to 2.2-fold increase in the cellulase, xylanase, and lichenase activities in comparison with the control (Cel44C-$Man26A_{P558}$). The optimum cellulase, linchenase, and xylanase activities of ${\beta}$-glycosyl hydrolase were observed at pH 7.0, pH 7.0 and pH 6.0, respectively. These results, therefore, suggest that the amino acid residue Ala438 plays important roles in the enhancement of the activity of multifunctional ${\beta}$-glycosyl hydrolase.

• Journal of Life Science
• /
• v.23 no.10
• /
• pp.1192-1198
• /
• 2013

To improve yeast strains for bioethanol production, yeasts with ethanol tolerance, thermotolerance, and ${\beta}$-1,3-glucanase activity were bred using yeast genome shuffling. Saccharomyces cerevisiae $BY4742{\Delta}exg1$/pAInu-exgA, which has extracellular ${\beta}$-1,3-glucanase activity, and the Aspergillus oryzae and S. cerevisiae YKY020 strains, which exhibit ethanol tolerance and thermotolerance, were fused by yeast protoplast fusion. Following cell fusion, four candidate cells (No. 3, 9, 11, and 12 strains) showing thermotolerance at $40^{\circ}C$ were selected, and their ethanol tolerance (7% ethanol concentration) and ${\beta}$-1,3-glucanase activity were subsequently analyzed. All the phenotypes of the two parent cells were simultaneously expressed in one (No. 11) of the four candidate cells, and this strain was called BYK-F11. The BYK-F11 fused cell showed enhanced cell growth, ethanol tolerance, ${\beta}$-1,3-glucanase activity, and ethanol productivity compared with the $BY4742{\Delta}exg1$/pAInu-exgA and YKY020 strains. The results prove that a new yeast strain with different characters and the same mating type can be easily bred by protoplast fusion of yeasts.

• 한국생물공학회:학술대회논문집
• /
• 2005.04a
• /
• pp.135-135
• /
• 2005

• The Journal of Korean Institute of Communications and Information Sciences
• /
• v.25 no.4B
• /
• pp.743-754
• /
• 2000

In this paper, we propose wavelet transform image compression method using shuffling and bit plane correlation. Proposed method is that original image decompose into multiresolutions using biorthogonal wavelet transform with linear phase response property and decomposed subbands are classified by maximum classification gain. And classified data sets in each subband are quantized using arbitrary set optimum bit allocation method. Quantized data sets in each subband are shuffled and context based bit plane arithmetic encoded .In context based bit plane arithmetic encoding, the context for each subband is not assigned uniformly, but assigned according to maximum correlation direction. Our results are comparable, or superior for some images at low rates, to published state-of-the-art coders.

• Journal of Microbiology
• /
• v.45 no.6
• /
• pp.572-577
• /
• 2007

To enhance therapeutic potential of murine monoclonal antibody, humanization by CDR grafting is usually used to reduce immunogenic mouse residues. Most humanized antibodies still have mouse residues critical for antigen binding, but the mouse residues may evoke immune responses in humans. Previously, we constructed a new humanized version (AKA) of mouse CC49 antibody specific for tumor-associated glycoprotein, TAG-72. In this study, to select a completely human antibody light chain against TAG-72, guided selection strategy using phage display was used. The heavy chain variable region (VH) of AKA was used to guide the selection of a human TAG-72-specific light chain variable region (VL) from a human VL repertoire constructed from human PBL. Most of the selected VLs were identified to be originated from the members of the human germline VK1 family, whereas the VL of AKA is more homologous to the VK4 family. Competition binding assay of the selected Fabs with mouse CC49 suggested that the epitopes of the Fabs overlap with that of CC49. In addition, they showed better antigen-binding affinity compared to parental AKA. The selected human VLs may be used to guide the selection of human VHs to get completely human anti-TAG72 antibody.

• Journal of Information Processing Systems
• /
• v.9 no.2
• /
• pp.271-286
• /
• 2013

Recently, a pixel-chaotic-shuffling (PCS) method has been proposed by Huang et al. for encrypting color images using multiple chaotic systems like the Henon, the Lorenz, the Chua, and the Rossler systems. All of which have great encryption performance. The authors claimed that their pixel-chaotic-shuffle (PCS) encryption method has high confidential security. However, the security analysis of the PCS method against the chosen-plaintext attack (CPA) and known-plaintext attack (KPA) performed by Solak et al. successfully breaks the PCS encryption scheme without knowing the secret key. In this paper we present an improved shuffling pattern for the plaintext image bits to make the cryptosystem proposed by Huang et al. resistant to chosen-plaintext attack and known-plaintext attack. The modifications in the existing PCS encryption method are proposed to improve its security performance against the potential attacks described above. The Number of Pixel Change Rate (NPCR), Unified Average Changed Intensity (UACI), information entropy, and correlation coefficient analysis are performed to evaluate the statistical performance of the modified PCS method. The simulation analysis reveals that the modified PCS method has better statistical features and is more resistant to attacks than Huang et al.'s PCS method.

• ETRI Journal
• /
• v.33 no.6
• /
• pp.935-944
• /
• 2011

As a growing number of individuals are exposed to surveillance cameras, the need to prevent captured videos from being used inappropriately has increased. Privacy-related information can be protected through video encryption during transmission or storage, and several algorithms have been proposed for such purposes. However, the simple way of evaluating the security by counting the number of brute-force trials is not proper for measuring the security of video encryption algorithms, considering that attackers can devise specially crafted attacks for specific purposes by exploiting the characteristics of the target video codec. In this paper, we introduce a new attack for recovering contour information from encrypted H.264 video. The attack can thus be used to extract face outlines for the purpose of personal identification. We analyze the security of previous video encryption schemes against the proposed attack and show that the security of these schemes is lower than expected in terms of privacy protection. To enhance security, an advanced block shuffling method is proposed, an analysis of which shows that it is more secure than the previous method and can be an improvement against the proposed attack.