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4,304 results on '"Shin, Jin"'

4. General Evaluation of EtherCAT-Based Techniques in Various Industrial Systems: Review and Applications

Author

Bui, The Tri, Shin, Jin-Ho, Ngo, Ha Quang Thinh, Akan, Ozgur, Editorial Board Member, Bellavista, Paolo, Editorial Board Member, Cao, Jiannong, Editorial Board Member, Coulson, Geoffrey, Editorial Board Member, Dressler, Falko, Editorial Board Member, Ferrari, Domenico, Editorial Board Member, Gerla, Mario, Editorial Board Member, Kobayashi, Hisashi, Editorial Board Member, Palazzo, Sergio, Editorial Board Member, Sahni, Sartaj, Editorial Board Member, Shen, Xuemin, Editorial Board Member, Stan, Mircea, Editorial Board Member, Jia, Xiaohua, Editorial Board Member, Zomaya, Albert Y., Editorial Board Member, Cong Vinh, Phan, editor, and Thanh Tung, Nguyen, editor

Published
2024
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8. Selection and adaptive introgression guided the complex evolutionary history of the European common bean

Author

Bellucci, Elisa, Benazzo, Andrea, Xu, Chunming, Bitocchi, Elena, Rodriguez, Monica, Alseekh, Saleh, Di Vittori, Valerio, Gioia, Tania, Neumann, Kerstin, Cortinovis, Gaia, Frascarelli, Giulia, Murube, Ester, Trucchi, Emiliano, Nanni, Laura, Ariani, Andrea, Logozzo, Giuseppina, Shin, Jin Hee, Liu, Chaochih, Jiang, Liang, Ferreira, Juan José, Campa, Ana, Attene, Giovanna, Morrell, Peter L, Bertorelle, Giorgio, Graner, Andreas, Gepts, Paul, Fernie, Alisdair R, Jackson, Scott A, and Papa, Roberto

Subjects
Biological Sciences, Genetics, Human Genome, Humans, Phaseolus, Genetic Variation, Genotype, Biological Evolution, Hybridization, Genetic
Abstract

Domesticated crops have been disseminated by humans over vast geographic areas. Common bean (Phaseolus vulgaris L.) was introduced in Europe after 1492. Here, by combining whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarro's expedition to northern Peru in 1529. We reveal that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe.

Published
2023

13. The Prostate Cancer Androgen Receptor Cistrome in African American Men Associates with Upregulation of Lipid Metabolism and Immune Response.

Author

Berchuck, Jacob, Adib, Elio, Abou Alaiwi, Sarah, Dash, Amit, Shin, Jin, Lowder, Dallin, McColl, Collin, Castro, Patricia, Carelli, Ryan, Benedetti, Elisa, Deng, Jenny, Robertson, Matthew, Baca, Sylvan, Bell, Connor, McClure, Heather, El Zarif, Talal, Davidsohn, Matthew, Lakshminarayanan, Gitanjali, Rizwan, Kinza, Skapura, Darlene, Grimm, Sandra, Davis, Christel, Ehli, Erik, Kelleher, Kaitlin, Seo, Ji-Heui, Mitsiades, Nicholas, Coarfa, Cristian, Pomerantz, Mark, Loda, Massimo, Ittmann, Michael, Freedman, Matthew, and Kaochar, Salma

Subjects
Black or African American, Humans, Immunity, Lipid Metabolism, Male, Prostatic Neoplasms, Receptors, Androgen, Up-Regulation
Abstract

UNLABELLED: African-American (AA) men are more likely to be diagnosed with and die from prostate cancer than European American (EA) men. Despite the central role of the androgen receptor (AR) transcription factor in prostate cancer, little is known about the contribution of epigenetics to observed racial disparities. We performed AR chromatin immunoprecipitation sequencing on primary prostate tumors from AA and EA men, finding that sites with greater AR binding intensity in AA relative to EA prostate cancer are enriched for lipid metabolism and immune response genes. Integration with transcriptomic and metabolomic data demonstrated coinciding upregulation of lipid metabolism gene expression and increased lipid levels in AA prostate cancer. In a metastatic prostate cancer cohort, upregulated lipid metabolism associated with poor prognosis. These findings offer the first insights into ancestry-specific differences in the prostate cancer AR cistrome. The data suggest a model whereby increased androgen signaling may contribute to higher levels of lipid metabolism, immune response, and cytokine signaling in AA prostate tumors. Given the association of upregulated lipogenesis with prostate cancer progression, our study provides a plausible biological explanation for the higher incidence and aggressiveness of prostate cancer observed in AA men. SIGNIFICANCE: With immunotherapies and inhibitors of metabolic enzymes in clinical development, the altered lipid metabolism and immune response in African-American men provides potential therapeutic opportunities to attenuate racial disparities in prostate cancer.

Published
2022

14. Pseudo-Differential Neural Operator: Generalized Fourier Neural Operator for Learning Solution Operators of Partial Differential Equations

Author

Shin, Jin Young, Lee, Jae Yong, and Hwang, Hyung Ju

Subjects
Computer Science - Machine Learning, Mathematics - Numerical Analysis, 35S05, 47G30, 68U07
Abstract

Learning the mapping between two function spaces has garnered considerable research attention. However, learning the solution operator of partial differential equations (PDEs) remains a challenge in scientific computing. Fourier neural operator (FNO) was recently proposed to learn solution operators, and it achieved an excellent performance. In this study, we propose a novel \textit{pseudo-differential integral operator} (PDIO) to analyze and generalize the Fourier integral operator in FNO. PDIO is inspired by a pseudo-differential operator, which is a generalized differential operator characterized by a certain symbol. We parameterize this symbol using a neural network and demonstrate that the neural network-based symbol is contained in a smooth symbol class. Subsequently, we verify that the PDIO is a bounded linear operator, and thus is continuous in the Sobolev space. We combine the PDIO with the neural operator to develop a \textit{pseudo-differential neural operator} (PDNO) and learn the nonlinear solution operator of PDEs. We experimentally validate the effectiveness of the proposed model by utilizing Darcy flow and the Navier-Stokes equation. The obtained results indicate that the proposed PDNO outperforms the existing neural operator approaches in most experiments., Comment: 23 pages, 13 figures

Published
2022

15. Solving PDE-constrained Control Problems Using Operator Learning

Author

Hwang, Rakhoon, Lee, Jae Yong, Shin, Jin Young, and Hwang, Hyung Ju

Subjects
Mathematics - Optimization and Control, Computer Science - Artificial Intelligence, Computer Science - Machine Learning, Mathematics - Numerical Analysis, Physics - Computational Physics, 68U07
Abstract

The modeling and control of complex physical systems are essential in real-world problems. We propose a novel framework that is generally applicable to solving PDE-constrained optimal control problems by introducing surrogate models for PDE solution operators with special regularizers. The procedure of the proposed framework is divided into two phases: solution operator learning for PDE constraints (Phase 1) and searching for optimal control (Phase 2). Once the surrogate model is trained in Phase 1, the optimal control can be inferred in Phase 2 without intensive computations. Our framework can be applied to both data-driven and data-free cases. We demonstrate the successful application of our method to various optimal control problems for different control variables with diverse PDE constraints from the Poisson equation to Burgers' equation., Comment: 15 pages, 12 figures. Published as a conference paper at Thirty-Sixth AAAI Conference on Artificial Intelligence (AAAI 2022)

Published
2021
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18. Genotype-phenotype correlations in valosin-containing protein disease: a retrospective muticentre study.

Author

Schiava, Marianela, Ikenaga, Chiseko, Villar-Quiles, Rocío, Caballero-Ávila, Marta, Topf, Ana, Nishino, Ichizo, Kimonis, Virginia, Udd, Bjarne, Schoser, Benedikt, Zanoteli, Edmar, Souza, Paulo, Tasca, Giorgio, Lloyd, Thomas, Lopez-de Munain, Adolfo, Paradas, Carmen, Pegoraro, Elena, Nadaj-Pakleza, Aleksandra, De Bleecker, Jan, Badrising, Umesh, Alonso-Jiménez, Alicia, Kostera-Pruszczyk, Anna, Miralles, Francesc, Shin, Jin-Hong, Bevilacqua, Jorge, Olivé, Montse, Vorgerd, Matthias, Kley, Rudi, Brady, Stefen, Williams, Timothy, Domínguez-González, Cristina, Papadimas, George, Warman-Chardon, Jodi, Claeys, Kristl, de Visser, Marianne, Muelas, Nuria, LaForet, Pascal, Malfatti, Edoardo, Alfano, Lindsay, Nair, Sruthi, Manousakis, Georgios, Kushlaf, Hani, Harms, Matthew, Nance, Christopher, Ramos-Fransi, Alba, Rodolico, Carmelo, Hewamadduma, Channa, Cetin, Hakan, García-García, Jorge, Pál, Endre, Farrugia, Maria, Lamont, Phillipa, Quinn, Colin, Nedkova-Hristova, Velina, Peric, Stojan, Luo, Sushan, Oldfors, Anders, Taylor, Kate, Ralston, Stuart, Stojkovic, Tanya, Weihl, Conrad, and Diaz-Manera, Jordi

Subjects
FRONTOTEMPORAL DEMENTIA, GENETICS, INCL BODY MYOSITIS, MUSCLE DISEASE, MYOPATHY
Abstract

BACKGROUND: Valosin-containing protein (VCP) disease, caused by mutations in the VCP gene, results in myopathy, Pagets disease of bone (PBD) and frontotemporal dementia (FTD). Natural history and genotype-phenotype correlation data are limited. This study characterises patients with mutations in VCP gene and investigates genotype-phenotype correlations. METHODS: Descriptive retrospective international study collecting clinical and genetic data of patients with mutations in the VCP gene. RESULTS: Two hundred and fifty-five patients (70.0% males) were included in the study. Mean age was 56.8±9.6 years and mean age of onset 45.6±9.3 years. Mean diagnostic delay was 7.7±6 years. Symmetric lower limb weakness was reported in 50% at onset progressing to generalised muscle weakness. Other common symptoms were ventilatory insufficiency 40.3%, PDB 28.2%, dysautonomia 21.4% and FTD 14.3%. Fifty-seven genetic variants were identified, 18 of these no previously reported. c.464G>A (p.Arg155His) was the most frequent variant, identified in the 28%. Full time wheelchair users accounted for 19.1% with a median time from disease onset to been wheelchair user of 8.5 years. Variant c.463C>T (p.Arg155Cys) showed an earlier onset (37.8±7.6 year) and a higher frequency of axial and upper limb weakness, scapular winging and cognitive impairment. Forced vital capacity (FVC) below 50% was as risk factor for being full-time wheelchair user, while FVC

Published
2022

19. Creation and annihilation of mobile fractional solitons in atomic chains

Author

Park, Jae Whan, Do, Eui Hwan, Shin, Jin Sung, Song, Sun Kyu, Stetsovych, Oleksandr, Jelinek, Pavel, and Yeom, Han Woong

Subjects
Condensed Matter - Materials Science, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Localized modes in one dimensional topological systems, such as Majonara modes in topological superconductors, are promising platforms for robust information processing. In one dimensional topological insulators, mobile topological solitons are expected but have not been fully realized yet. We discover fractionalized phase defects moving along trimer silicon atomic chains formed along step edges of a vicinal silicon surface. Tunneling microscopy identifies local defects with phase shifts of 2{\pi}/3 and 4{\pi}/3 with their electronic states within the band gap and with their motions activated above 100 K. Theoretical calculations reveal the topological soliton origin of the phase defects with fractional charges of {\pm}2e/3 and {\pm}4e/3. An individual soliton can be created and annihilated at a desired location by current pulse from the probe tip. Mobile and manipulatable topological solitons discovered here provide a new platform of robustly-protected informatics with extraordinary functionalities., Comment: 18 pages, 4 figures

Published
2021
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20. Endosomal Arl4A attenuates EGFR degradation by binding to the ESCRT-II component VPS36

Author

Shin-Jin Lin, Ming-Chieh Lin, Tsai-Jung Liu, Yueh-Tso Tsai, Ming-Ting Tsai, and Fang-Jen S. Lee

Subjects
Science
Abstract

Abstract Ligand-induced epidermal growth factor receptor (EGFR) endocytosis followed by endosomal EGFR signaling and lysosomal degradation plays important roles in controlling multiple biological processes. ADP-ribosylation factor (Arf)-like protein 4 A (Arl4A) functions at the plasma membrane to mediate cytoskeletal remodeling and cell migration, whereas its localization at endosomal compartments remains functionally unknown. Here, we report that Arl4A attenuates EGFR degradation by binding to the endosomal sorting complex required for transport (ESCRT)-II component VPS36. Arl4A plays a role in prolonging the duration of EGFR ubiquitinylation and deterring endocytosed EGFR transport from endosomes to lysosomes under EGF stimulation. Mechanistically, the Arl4A-VPS36 direct interaction stabilizes VPS36 and ESCRT-III association, affecting subsequent recruitment of deubiquitinating-enzyme USP8 by CHMP2A. Impaired Arl4A-VPS36 interaction enhances EGFR degradation and clearance of EGFR ubiquitinylation. Together, we discover that Arl4A negatively regulates EGFR degradation by binding to VPS36 and attenuating ESCRT-mediated late endosomal EGFR sorting.

Published
2023
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21. Inhibition of GATA2 in prostate cancer by a clinically available small molecule.

Author

Kaochar, Salma, Rusin, Aleksandra, Foley, Christopher, Rajapakshe, Kimal, Robertson, Matthew, Skapura, Darlene, Mason, Cammy, Berman De Ruiz, Karen, Tyryshkin, Alexey, Deng, Jenny, Shin, Jin, Fiskus, Warren, Dong, Jianrong, Huang, Shixia, Navone, Nora, Davis, Christel, Ehli, Erik, Coarfa, Cristian, and Mitsiades, Nicholas

Subjects
Dilazep, GATA2, c-MYC, castration-resistance, prostate cancer, Cell Line, Tumor, Chromatin, Dilazep, GATA2 Transcription Factor, Gene Expression Regulation, Neoplastic, Humans, Male, Oncogenes, Prostatic Neoplasms, Castration-Resistant, Receptors, Androgen
Abstract

Castration-resistant prostate cancer (CRPC) remains highly lethal and in need of novel, actionable therapeutic targets. The pioneer factor GATA2 is a significant prostate cancer (PC) driver and is linked to poor prognosis. GATA2 directly promotes androgen receptor (AR) gene expression (both full-length and splice-variant) and facilitates AR binding to chromatin, recruitment of coregulators, and target gene transcription. Unfortunately, there is no clinically applicable GATA2 inhibitor available at the moment. Using a bioinformatics algorithm, we screened in silico 2650 clinically relevant drugs for a potential GATA2 inhibitor. Validation studies used cytotoxicity and proliferation assays, global gene expression analysis, RT-qPCR, reporter assay, reverse phase protein array analysis (RPPA), and immunoblotting. We examined target engagement via cellular thermal shift assay (CETSA), ChIP-qPCR, and GATA2 DNA-binding assay. We identified the vasodilator dilazep as a potential GATA2 inhibitor and confirmed on-target activity via CETSA. Dilazep exerted anticancer activity across a broad panel of GATA2-dependent PC cell lines in vitro and in a PDX model in vivo. Dilazep inhibited GATA2 recruitment to chromatin and suppressed the cell-cycle program, transcriptional programs driven by GATA2, AR, and c-MYC, and the expression of several oncogenic drivers, including AR, c-MYC, FOXM1, CENPF, EZH2, UBE2C, and RRM2, as well as of several mediators of metastasis, DNA damage repair, and stemness. In conclusion, we provide, via an extensive compendium of methodologies, proof-of-principle that a small molecule can inhibit GATA2 function and suppress its downstream AR, c-MYC, and other PC-driving effectors. We propose GATA2 as a therapeutic target in CRPC.

Published
2021

24. Prior Preference Learning from Experts:Designing a Reward with Active Inference

Author

Shin, Jin young, Kim, Cheolhyeong, and Hwang, Hyung Ju

Subjects
Computer Science - Machine Learning
Abstract

Active inference may be defined as Bayesian modeling of a brain with a biologically plausible model of the agent. Its primary idea relies on the free energy principle and the prior preference of the agent. An agent will choose an action that leads to its prior preference for a future observation. In this paper, we claim that active inference can be interpreted using reinforcement learning (RL) algorithms and find a theoretical connection between them. We extend the concept of expected free energy (EFE), which is a core quantity in active inference, and claim that EFE can be treated as a negative value function. Motivated by the concept of prior preference and a theoretical connection, we propose a simple but novel method for learning a prior preference from experts. This illustrates that the problem with inverse RL can be approached with a new perspective of active inference. Experimental results of prior preference learning show the possibility of active inference with EFE-based rewards and its application to an inverse RL problem., Comment: This paper is accepted to Neurocomputing

Published
2021

26. What is the impact of one’s chronic illness on his or her spouse’s future chronic illness: a community-based prospective cohort study

Author

An, Hoyoung, Yang, Hee Won, Oh, Dae Jong, Lim, Eunji, Shin, Jin, Moon, Dong Gyu, Suh, Seung Wan, Byun, Seonjeong, Kim, Tae Hui, Kwak, Kyung Phil, Kim, Bong Jo, Kim, Shin Gyeom, Kim, Jeong Lan, Moon, Seok Woo, Park, Joon Hyuk, Ryu, Seung-Ho, Lee, Dong Woo, Lee, Seok Bum, Lee, Jung Jae, Jhoo, Jin Hyeong, Bae, Jong Bin, Han, Ji Won, and Kim, Ki Woong

Published
2023
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28. Lrig1-expression confers suppressive function to CD4+ cells and is essential for averting autoimmunity via the Smad2/3/Foxp3 axis

Author

Moon, Jae-Seung, Ho, Chun-Chang, Park, Jong-Hyun, Park, Kyungsoo, Shin, Bo-Young, Lee, Su-Hyeon, Sequeira, Ines, Mun, Chin Hee, Shin, Jin-Su, Kim, Jung-Ho, Kim, Beom Seok, Noh, Jin-Wook, Lee, Eui-Seon, Son, Ji Young, Kim, Yuna, lee, Yeji, Cho, Hee, So, SunHyeon, Park, Jiyoon, Choi, Eunsu, Oh, Jong-Won, Lee, Sang-Won, Morio, Tomohiro, Watt, Fiona M., Seong, Rho Hyun, and Lee, Sang-Kyou

Published
2023
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