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Spc1 regulates substrate selection for signal peptidase [article]

Chewon Yim, Yeonji Chung, Jeesoo Kim, IngMarie Nilsson, Jong-Seo Kim, Hyun (Joy) Kim
2021 bioRxiv   pre-print
and Communications Technology of Korea (IBS-547 R008-D1) to Jeesoo Kim and Jong-Seo Kim.  ...  Kim, Y. Jung, S.D. Jeong, and H. Kim. 2018.  ... 
doi:10.1101/2021.02.02.429376 fatcat:mgvfuwp62rffliipcdzupw4vhm

Dynamic Graph Generation Network: Generating Relational Knowledge from Diagrams [article]

Daesik Kim, Youngjoon Yoo, Jeesoo Kim, Sangkuk Lee, Nojun Kwak
2017 arXiv   pre-print
In this work, we introduce a new algorithm for analyzing a diagram, which contains visual and textual information in an abstract and integrated way. Whereas diagrams contain richer information compared with individual image-based or language-based data, proper solutions for automatically understanding them have not been proposed due to their innate characteristics of multi-modality and arbitrariness of layouts. To tackle this problem, we propose a unified diagram-parsing network for generating
more » ... nowledge from diagrams based on an object detector and a recurrent neural network designed for a graphical structure. Specifically, we propose a dynamic graph-generation network that is based on dynamic memory and graph theory. We explore the dynamics of information in a diagram with activation of gates in gated recurrent unit (GRU) cells. On publicly available diagram datasets, our model demonstrates a state-of-the-art result that outperforms other baselines. Moreover, further experiments on question answering shows potentials of the proposed method for various applications.
arXiv:1711.09528v1 fatcat:odt4vse6ozfbjkaq2362hf74e4

The SARS-CoV-2 RNA interactome [article]

Sungyul Lee, Young-suk Lee, Yeon Choi, Ahyeon Son, Youngran Park, Kyung-Min Lee, Jeesoo Kim, Jong-Seo Kim, V. Narry Kim
2020 bioRxiv   pre-print
The sgRNAs are more abundant than the gRNA (Kim et al., 2020a) .  ...  ., 2015) that encode structural proteins (S, E, M, and N) and accessory proteins (3a, 3c, 6, 7a, 7b, 8 , and 9b) (Kim et al., 2020a) .  ... 
doi:10.1101/2020.11.02.364497 fatcat:hwibdczgtfdcnelsxumnanjgva

Normalization Matters in Weakly Supervised Object Localization [article]

Jeesoo Kim, Junsuk Choe, Sangdoo Yun, Nojun Kwak
2021 arXiv   pre-print
Weakly-supervised object localization (WSOL) enables finding an object using a dataset without any localization information. By simply training a classification model using only image-level annotations, the feature map of the model can be utilized as a score map for localization. In spite of many WSOL methods proposing novel strategies, there has not been any de facto standard about how to normalize the class activation map (CAM). Consequently, many WSOL methods have failed to fully exploit
more » ... r own capacity because of the misuse of a normalization method. In this paper, we review many existing normalization methods and point out that they should be used according to the property of the given dataset. Additionally, we propose a new normalization method which substantially enhances the performance of any CAM-based WSOL methods. Using the proposed normalization method, we provide a comprehensive evaluation over three datasets (CUB, ImageNet and OpenImages) on three different architectures and observe significant performance gains over the conventional min-max normalization method in all the evaluated cases.
arXiv:2107.13221v1 fatcat:yevz4fnl3fbddjpjbnm4c237dy

An Automated Vulnerability Detection and Remediation Method for Software Security

Jeesoo Jurn, Taeeun Kim, Hwankuk Kim
2018 Sustainability  
As hacking techniques become more sophisticated, vulnerabilities have been gradually increasing. Between 2010 and 2015, around 80,000 vulnerabilities were newly registered in the CVE (Common Vulnerability Enumeration), and the number of vulnerabilities has continued to rise. While the number of vulnerabilities is increasing rapidly, the response to them relies on manual analysis, resulting in a slow response speed. It is necessary to develop techniques that can detect and patch vulnerabilities
more » ... utomatically. This paper introduces a trend of techniques and tools related to automated vulnerability detection and remediation. We propose an automated vulnerability detection method based on binary complexity analysis to prevent a zero-day attack. We also introduce an automatic patch generation method through PLT/GOT table modification to respond to zero-day vulnerabilities.
doi:10.3390/su10051652 fatcat:752sfczsgrdwniw4nlez6jfzaq

StackNet: Stacking Parameters for Continual learning [article]

Jangho Kim, Jeesoo Kim, Nojun Kwak
2020 arXiv   pre-print
Training a neural network for a classification task typically assumes that the data to train are given from the beginning. However, in the real world, additional data accumulate gradually and the model requires additional training without accessing the old training data. This usually leads to the catastrophic forgetting problem which is inevitable for the traditional training methodology of neural networks. In this paper, we propose a continual learning method that is able to learn additional
more » ... sks while retaining the performance of previously learned tasks by stacking parameters. Composed of two complementary components, the index module and the StackNet, our method estimates the index of the corresponding task for an input sample with the index module and utilizes a particular portion of StackNet with this index. The StackNet guarantees no degradation in the performance of the previously learned tasks and the index module shows high confidence in finding the origin of an input sample. Compared to the previous work of PackNet, our method is competitive and highly intuitive.
arXiv:1809.02441v3 fatcat:gt5s5op5yvgkliwot5yyzrquty

ERH as a component of the Microprocessor facilitates the maturation of suboptimal microRNAs [article]

S. Chul Kwon, Harim Jang, Jihye Yang, Jeesoo Kim, S. Chan Baek, Jong-Seo Kim, V. Narry Kim
2020 bioRxiv   pre-print
ACKNOWLEDGEMENTS We thank Eunji Kim  ... 
doi:10.1101/2020.05.13.093278 fatcat:5g2em4y3kzattlk4vpee6ogn3m

Spc1 regulates the signal peptidase-mediated processing of membrane proteins

Chewon Yim, Yeonji Chung, Jeesoo Kim, IngMarie Nilsson, Jong-Seo Kim, Hyun Kim
2021 Journal of Cell Science  
Signal peptidase (SPase) cleaves the signal sequences (SSs) of secretory precursors. It contains an evolutionarily conserved membrane protein subunit, Spc1 that is dispensable for the catalytic activity of SPase, and its role remains unknown. In the present study, we investigated the function of yeast Spc1. First, we set up an in vivo SPase cleavage assay using secretory protein CPY variants with SSs modified in the n and h regions. When comparing the SS cleavage efficiencies of these variants
more » ... n cells with or without Spc1, we found that signal-anchored sequences became more susceptible to cleavage by SPase without Spc1. Further, SPase-mediated processing of model membrane proteins was enhanced in the absence of but reduced upon overexpression of Spc1. Spc1 was co-immunoprecipitated with proteins carrying uncleaved signal-anchored or transmembrane (TM) segments. Taken together, these results suggest that Spc1 protects TM segments from SPase action, thereby sharpening substrate selection for SPase and acting as a negative regulator for the SPase-mediated processing of membrane proteins.
doi:10.1242/jcs.258936 pmid:34125229 pmcid:PMC8277137 fatcat:yhau3vo2mrf4zoxm6dpyisckrq

Enzymatic Production of Steviol Glucosides Using β-Glucosidase and Their Applications [chapter]

Thi Thanh Hanh Nguyen, Changseop Seo, So-Hyung Kwak, Jeesoo Kim, Hee-Kyoung Kang, Seong-Bo Kim, Doman Kim
2019 Enzymes in Food Biotechnology  
Tanaka et al., 1981 Reb, rebaudioside; Glc, glucosyl; Rha, rhamnosyl; Xyl, xylosyl; Sweetness*, times sweeter than sucrose at concentration of 0.025%. ENZYMATIC MODIFICATION OF STEVIOL GLUCOSIDES
doi:10.1016/b978-0-12-813280-7.00023-2 fatcat:paqjrpoxofafrhuye5qhsvot6u

Formation of Thermally Stable Bulk Heterojunction by Reducing the Polymer and Fullerene Intermixing

Yoonhee Jang, Yun Ju Cho, Minjung Kim, Jeesoo Seok, Hyungju Ahn, Kyungkon Kim
2017 Scientific Reports  
A morphologically stable bulk heterojunction (BHJ) with a large heterojunction area is prepared by reducing the portion of the small band gap polymer (PTB7) and fullerene intermixture through a sequential deposition (SqD) of the nanostructured PTB7 and the fullerene layer. The nanostructured PTB7 layer is prepared using a ternary solvent composed of chlorobenzene, 1,8-diiodooctane (DIO) and 1-chloronaphthalene (1-CN). Adding DIO and 1-CN enhances the ordering of PTB7 chains and results in a
more » ... structured polymer surface. The grazing incidence X-ray diffraction results reveal that the SqD of the nanostructured PTB7 and fullerene layers forms the BHJ with little intermixing between the polymer and the fullerene domains compared to the BHJ formed by the deposition of the blended PTB7 and fullerene solution (BSD). The OPV utilizing the SqD processed BHJ (SqD-OPV) exhibits a power conversion efficiency (PCE) of 7.43%, which is similar to that when the BSD processed BHJ (BSD-OPV) is utilized. Furthermore, the SqD-OPV exhibits an excellent thermal stability. The SqD-OPV maintains its initial PCE even after thermal annealing at 140 °C for 10 days, whereas the BSD-OPV maintains 78% of its initial efficiency under the same condition. The bulk heterojunction (BHJ) is the most widely used photo-active layer system for organic photovoltaic (OPV) devices 1-3 . The BHJ is mostly formed by the blended solution deposition (BSD), where a BHJ is prepared by depositing a blended solution of electron donating polymer and electron accepting organic semiconductors. The fullerene derivatives have been used mainly as the electron accepting organic semiconductors. Nowadays, many efficient non-fullerene acceptors have been reported to achieve excellent solar cell performance in the BHJ OPV 4 . The BSD process is effective in forming the heterojunction with a large surface area. However, delicate controls of the processing conditions (e.g., donor to acceptor ratio, amount of processing additives, types of solvents, processing temperature, and additional annealing process) are required to maximize the solar cell performance by inducing the nano-scale phase separation of the donor and the acceptor materials 5 . An alternative method of forming the BHJ through sequential deposition (SqD) has recently been reported by several researchers 6-12 . The SqD process is more flexible in finding an optimized condition because the system can be optimized by independently controlling the thickness of each layer. However, finding a method of enhancing the heterojunction area and a proper solution for the top-layer that does not dissolve the bottom-layer are required to achieve efficient SqD processed OPVs (SqD-OPV). Yang et al. claimed that the SqD-OPV based on P3HT/PCBM had the potential to show a better performance than a BSD processed OPV (BSD-OPV) because of a significant reduction in the bimolecular charge recombination 5 . The Schwartz group found that the BHJ morphology formed by the SqD process was almost identical to that formed by the BSD process and could be controlled using tailored semi-orthogonal solvent blends 7 . In terms of the BHJ morphology, pure polymer and fullerene domains and polymer and fullerene intermixture were reported to co-exist in the BHJ prepared by the BSD 13-16 . The intermixture domain may cause the morphological instability of the BHJ processed by the BSD 16 . Meanwhile, the polymer crystallinity was not disturbed by the SqD of fullerene, which would help in enhancing the morphological stability 12 . However, as the BSD process does, the SqD-OPVs require an additional thermal annealing step to obtain a large heterojunction area because of the ineffective penetration of fullerenes into the polymer layer. The post thermal annealing process might form polymer and fullerene intermixtures. Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 SCiENtifiC RePoRTS | 7: 9690 |
doi:10.1038/s41598-017-09167-4 pmid:28851926 pmcid:PMC5575051 fatcat:fsdlhzqyjjaovdg5omvrkxv53m

A Comprehensive Overhaul of Feature Distillation [article]

Byeongho Heo, Jeesoo Kim, Sangdoo Yun, Hyojin Park, Nojun Kwak, Jin Young Choi
2019 arXiv   pre-print
We investigate the design aspects of feature distillation methods achieving network compression and propose a novel feature distillation method in which the distillation loss is designed to make a synergy among various aspects: teacher transform, student transform, distillation feature position and distance function. Our proposed distillation loss includes a feature transform with a newly designed margin ReLU, a new distillation feature position, and a partial L2 distance function to skip
more » ... ant information giving adverse effects to the compression of student. In ImageNet, our proposed method achieves 21.65% of top-1 error with ResNet50, which outperforms the performance of the teacher network, ResNet152. Our proposed method is evaluated on various tasks such as image classification, object detection and semantic segmentation and achieves a significant performance improvement in all tasks. The code is available at https://sites.google.com/view/byeongho-heo/overhaul
arXiv:1904.01866v2 fatcat:r7yelxbwunezro4rqzfcedsr4e

Proteomic analysis of human synovial fluid reveals potential diagnostic biomarkers for ankylosing spondylitis

Ji-Hyun Lee, Jae Hun Jung, Jeesoo Kim, Won-Ki Baek, Jinseol Rhee, Tae-Hwan Kim, Sang-Hyon Kim, Kwang Pyo Kim, Chang-Nam Son, Jong-Seo Kim
2020 Clinical Proteomics  
Ankylosing spondylitis (AS) is a chronic inflammatory rheumatic disease affecting the axial skeleton and peripheral joints. The etiology of this disease remains poorly understood, but interactions between genetic and environmental factors have been implicated. The present study identified differentially expressed proteins in the synovial fluid (SF) of AS patients to elucidate the underlying cause of AS. A cohort of 40 SF samples from 10 AS and 10 each of rheumatoid arthritis (RA), gout, and
more » ... oarthritis (OA) patients were analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify differentially expressed proteins specific to AS. The label-free LC-MS/MS results were verified by western blotting. We identified 8 proteins that were > 1.5-fold upregulated in the SF of AS patients compared to that of the disease control groups, including HP, MMP1, MMP3, serum amyloid P-component (APCS), complement factor H-related protein 5 (CFHR5), mannose-binding lectin 2 (MBL2), complement component C9 (C9), and complement C4-A (C4A). CFHR5 and C9 were previously found in serum from AS patients, while APCS was previously found in SF as well as in serum. However, the present study has identified C4A, and MBL2 as potential AS biomarkers for the first time. The expression levels of MMP3, C9, and CFHR5 were verified in AS SF using western blotting. We performed quantitative comparative proteomic analysis using by LC-MS/MS of the SF from four disease states: RA, gout, and OA. This systematic comparison revealed novel differentially expressed proteins in AS SF, as well as two previously reported candidate biomarkers. We further verified the expression of MMP3, C9 and CFHR5 by western blot. These proteins may serve as diagnostic or prognostic biomarkers in patients with AS, and may thus improve the clinical outcomes of this serious disease.
doi:10.1186/s12014-020-09281-y pmid:32518534 pmcid:PMC7269004 fatcat:aonuvflbojepzpjwkkvet67if4

Dynamic tracking and identification of tissue-specific secretory proteins in the circulation of live mice [article]

Kwang-eun Kim, Isaac Park, Jeesoo Kim, Myeong-Gyun Kang, Won Gun Choi, Hyemi Shin, Jong-Seo Kim, Hyun-Woo Rhee, Jae Myoung Suh
2020 bioRxiv   pre-print
It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in Kim et al.  ...  The copyright holder for this this version posted October 13, 2020. ; https://doi.org/10.1101/2020.09.21.299198 doi: bioRxiv preprint Kim et al.Figure 1 Biotin Streptavidin-HRP Anti-V5 * * *  ... 
doi:10.1101/2020.09.21.299198 fatcat:k4yvgzkxmnftnlgorraxqwdrwu

Dynamic Graph Generation Network: Generating Relational Knowledge from Diagrams

Daesik Kim, YoungJoon Yoo, Jeesoo Kim, Sangkuk Lee, Nojun Kwak
2018 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition  
In this work, we introduce a new algorithm for analyzing a diagram, which contains visual and textual information in an abstract and integrated way. Whereas diagrams contain richer information compared with individual image-based or language-based data, proper solutions for automatically understanding them have not been proposed due to their innate characteristics of multi-modality and arbitrariness of layouts. To tackle this problem, we propose a unified diagram-parsing network for generating
more » ... nowledge from diagrams based on an object detector and a recurrent neural network designed for a graphical structure. Specifically, we propose a dynamic graph-generation network that is based on dynamic memory and graph theory. We explore the dynamics of information in a diagram with activation of gates in gated recurrent unit (GRU) cells. On publicly available diagram datasets, our model demonstrates a state-of-the-art result that outperforms other baselines. Moreover, further experiments on question answering shows potentials of the proposed method for various applications.
doi:10.1109/cvpr.2018.00438 dblp:conf/cvpr/KimYKLK18 fatcat:j5gyp63swzf35aclv2dtxzv4i4

Endomembrane systems are reorganized by ORF3a and Membrane (M) of SARS-CoV-2 [article]

Yun-Bin Lee, Minkyo Jung, Jeesoo Kim, Myeong-Gyun Kang, Chulhwan Kwak, Jong-Seo Kim, Ji-Young Mun, Hyun-Woo Rhee
2021 bioRxiv   pre-print
To investigate alterations in the host cell 332 secretome, we used recently developed method dubbed iSLET (in situ secretory protein labeling via ER-333 anchored TurboID) (Kim et al., 2020).  ... 
doi:10.1101/2021.06.01.446555 fatcat:swzssx5fzvgy5aebyuwnxp456i
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