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Готові списки джерел за темами / Motifs de surface / Статті в журналах

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Статті в журналах з теми "Motifs de surface"

Автор: Grafiati

Опубліковано: 7 липня 2024

Оновлено: 19 липня 2025

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1

SHRESTHA, NRIPENDRA L., YOUHEI KAWAGUCHI, and TAKENAO OHKAWA. "SUMOMO: A PROTEIN SURFACE MOTIF MINING MODULE." International Journal of Computational Intelligence and Applications 04, no. 04 (2004): 431–49. http://dx.doi.org/10.1142/s1469026804001392.

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Анотація:

Protein surface motifs, which can be defined as commonly appearing patterns of shape and physical properties in protein molecular surfaces, can be considered "possible active sites". We have developed a system for mining surface motifs: SUMOMO which consists of two phases: surface motif extraction and surface motif filtering. In the extraction phase, a given set of protein molecular surface data is divided into small surfaces called unit surfaces. After extracting several common unit surfaces as candidate motifs, they are repetitively merged into surface motifs. However, a large amount of surf

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2

Kumar, J., and M. S. Shunmugam. "Three-Dimensional Characterization of Engineering Surfaces Using Triangular Motifs." Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science 219, no. 9 (2005): 965–77. http://dx.doi.org/10.1243/095440605x31823.

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The functional behaviour of manufactured surfaces is influenced by the surface topography. Encouraged by the results obtained in the implementation of two-dimensional motifs for practical profiles, a few attempts have been made to arrive at areal motifs for characterization of the surfaces. In this paper, an approach for establishing three-dimensional motifs based on triangular motif is presented. The triangular motif is formed with three peaks and a deep valley between them. To represent the surface by significant motifs, initial motifs are combined using four rules that are extended from the

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3

Stephens, Edward B., Dusan Kunec, Wyatt Henke, et al. "The Role of the Tyrosine-Based Sorting Signals of the ORF3a Protein of SARS-CoV-2 in Intracellular Trafficking and Pathogenesis." Viruses 17, no. 4 (2025): 522. https://doi.org/10.3390/v17040522.

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The open reading frame 3a (ORF3a) is a protein important to the pathogenicity of SARS-CoV-2. The cytoplasmic domain of ORF3a has three canonical tyrosine-based sorting signals (160YNSV163, 211YYQL213, and 233YNKI236), and a previous study has indicated that mutation of the 160YNSV163 motif abrogated plasma membrane expression and inhibited ORF3a-induced apoptosis. Here, we have systematically removed all three tyrosine-based motifs and assessed the importance of each motif or combination of motifs in trafficking to the cell surface. Our results indicate that the 160YNSV163 motif alone was insu

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4

da Silva, Luiz C. B., and Efi Efrati. "Construction of exact minimal parking garages: nonlinear helical motifs in optimally packed lamellar structures." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 477, no. 2246 (2021): 20200891. http://dx.doi.org/10.1098/rspa.2020.0891.

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Minimal surfaces arise as energy minimizers for fluid membranes and are thus found in a variety of biological systems. The tight lamellar structures of the endoplasmic reticulum and plant thylakoids are comprised of such minimal surfaces in which right- and left-handed helical motifs are embedded in stoichiometry suggesting global pitch balance. So far, the analytical treatment of helical motifs in minimal surfaces was limited to the small-slope approximation where motifs are represented by the graph of harmonic functions. However, in most biologically and physically relevant regimes the inter

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5

Doshi, PD, and JF DiPersio. "Three conserved motifs in the extracellular domain of the human granulocyte-macrophage colony-stimulating factor receptor subunit are essential for ligand binding and surface expression." Blood 84, no. 8 (1994): 2539–53. http://dx.doi.org/10.1182/blood.v84.8.2539.2539.

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Abstract The receptor for the human granulocyte-macrophage colony-stimulating factor (GM-CSF) (GM-R) is a heterodimeric complex consisting of two subunits, GM-R alpha and GM-R beta. Structural analyses have shown a number of highly conserved amino acid motifs present in both GM-R alpha and GM-R beta. These motifs include QYFLY, CXW, XW, and WSXWS motifs in the extracellular domain; a conserved cysteine in the transmembrane domain; and the entire cytoplasmic domain, including the LXVLX box in the carboxy terminal region of the cytoplasmic domain. We have investigated the role of these motifs in

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6

Doshi, PD, and JF DiPersio. "Three conserved motifs in the extracellular domain of the human granulocyte-macrophage colony-stimulating factor receptor subunit are essential for ligand binding and surface expression." Blood 84, no. 8 (1994): 2539–53. http://dx.doi.org/10.1182/blood.v84.8.2539.bloodjournal8482539.

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Анотація:

The receptor for the human granulocyte-macrophage colony-stimulating factor (GM-CSF) (GM-R) is a heterodimeric complex consisting of two subunits, GM-R alpha and GM-R beta. Structural analyses have shown a number of highly conserved amino acid motifs present in both GM-R alpha and GM-R beta. These motifs include QYFLY, CXW, XW, and WSXWS motifs in the extracellular domain; a conserved cysteine in the transmembrane domain; and the entire cytoplasmic domain, including the LXVLX box in the carboxy terminal region of the cytoplasmic domain. We have investigated the role of these motifs in GM-R alp

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7

Kusuma, Wahyu Teja, Herman Tolle, and Ahmad Afif Supianto. "Augmented Reality Application to Efficiency the Process of Making Batik Motifs Using Vertex Marker." Journal of Information Technology and Computer Science 4, no. 3 (2019): 267. http://dx.doi.org/10.25126/jitecs.201943154.

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From the total time of making traditional Batik, the batik stage is the most time consuming because there are a lot of mistakes due to lack of carefulness when making batik motifs on cloth. To overcome the problem of making Batik motifs, this research utilizes the strengths and capabilities of Marker-Based Augmented Reality technology. The development of Marker-Based Augmented Reality applications is done by replacing digital objects with Batik motif images and markers attached to the fabric. Development of Marker-Based Augmented Reality applications using vertex markers to reproduce Batik mot

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8

Marsh, B. J., R. A. Alm, S. R. McIntosh, and D. E. James. "Molecular regulation of GLUT-4 targeting in 3T3-L1 adipocytes." Journal of Cell Biology 130, no. 5 (1995): 1081–91. http://dx.doi.org/10.1083/jcb.130.5.1081.

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Insulin stimulates glucose transport in muscle and adipose tissue by triggering the movement of the glucose transporter GLUT-4 from an intracellular compartment to the cell surface. Fundamental to this process is the intracellular sequestration of GLUT-4 in nonstimulated cells. Two distinct targeting motifs in the amino and carboxy termini of GLUT-4 have been previously identified by expressing chimeras comprised of portions of GLUT-4 and GLUT-1, a transporter isoform that is constitutively targeted to the cell surface, in heterologous cells. These motifs-FQQI in the NH2 terminus and LL in the

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9

Sarhan, Mohammed. "Ice nucleation protein as a bacterial surface display protein." Archives of Biological Sciences 63, no. 4 (2011): 943–48. http://dx.doi.org/10.2298/abs1104943s.

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Surface display technology can be defined as that phenotype (protein or peptide) which is linked to a genotype (DNA or RNA) through an appropriate anchoring motif. A bacterial surface display system is based on expressing recombinant proteins fused to sorting signals (anchoring motifs) that direct their incorporation on the cell surface.

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10

Monk, Brian C., and David R. K. Harding. "Peptide Motifs for Cell-Surface Intervention." BioDrugs 19, no. 4 (2005): 261–78. http://dx.doi.org/10.2165/00063030-200519040-00005.

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11

Mouli, M. S. S. Vinod, and Ashutosh Kumar Mishra. "Formation of the silver–flavin coordination polymers and their morphological studies." CrystEngComm 24, no. 12 (2022): 2221–25. http://dx.doi.org/10.1039/d2ce00071g.

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Herein we discuss the formation of 1-D polymeric motifs for the silver–flavin complex achieved via rare bidentate coordination for the modified flavin moiety. Further studies revealed facile transfer of the polymeric motif onto the surface.

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12

Kowalski, Maciej, Magdalena Wiśniewska, Paweł Karolczak, and Jozef Holubjak. "Possibilities of applying motif group parameters for description roughness of turned surfaces." MATEC Web of Conferences 244 (2018): 01028. http://dx.doi.org/10.1051/matecconf/201824401028.

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This article explores the methodology of assessing the applicability of roughness parameters from the motif group to the evaluation of one-way and periodic geometrical surface structures. The results of surface roughness measurements of aluminum samples turned with variable kinematic parameters were presented. Usability of using surface motifs in combination with selected parameters described in ISO standards for assessment of geometrical structures characteristic for longitudinal turning was shown.

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13

Ahmed Faraz. "Symbolic Significance of Star Motifs in Islamic Geometric Decoration and Contemporary Trademark Design in Pakistan." Al-Qamar 6, no. 3 (2023): 95–114. https://doi.org/10.53762/kgc7xx59.

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Geometric decoration in Islamic art has a special significance having symbolic meanings. Star motif is one of the most prominent shapes employed in these geometric decorations. These motifs, as they originated with spiritual essence in Persia around nineth century, were carried on as an influential factor in South Asian art, particularly Mughal art. The surface embellishments of the Mughal monuments are flooded with geometries having various types of star motifs. Interestingly, the contemporary trademark design in Pakistan reveals great influence from these geometric star motifs. Having a symb

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14

Lungu, Antonela, Maria Cristina Timar, Emanuela Carmen Beldean, Sergiu Valeriu Georgescu, and Camelia Coşereanu. "Adding Value to Maple (Acer pseudoplatanus) Wood Furniture Surfaces by Different Methods of Transposing Motifs from Textile Heritage." Coatings 12, no. 10 (2022): 1393. http://dx.doi.org/10.3390/coatings12101393.

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The present paper is part of an ongoing research project carried out to find methods to transpose traditional motifs from Romanian textile heritage to furniture ornamentation, as an additional method of preserving the motifs besides conventional conservation. Modern technology, such as Computer Numerical Control (CNC) routing or laser engraving can revive furniture ornamentation, eliminating manual labor and long execution time. Three methods were applied to transpose a bicolored motif from a traditional Romanian blouse from Transylvania onto the surface of maple wood furniture. The first meth

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15

Bourgeois-Daigneault, Marie-Claude, and Jacques Thibodeau. "Identification of a novel motif important for the activity of ring-type E3 ligases using MARCH1 as a model (100.52)." Journal of Immunology 186, no. 1_Supplement (2011): 100.52. http://dx.doi.org/10.4049/jimmunol.186.supp.100.52.

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Abstract The MARCH family of proteins are RING-CH type E3 ubiquitin ligases responsible for the ubiquitination and endocytosis of cell surface proteins related to immune response. We are particularty interested in MARCH1 and 8, two members of the family that are known to downregulate the cell surface expression of MHC II, CD86 , TfR and CD95. Canonical sorting motifs in the cytoplasmic portions of murine MARCH1 and human MARCH8 were identified and reported by others to be necessary for the function. We hypothesized that such motifs in human MARCH1 are important for it’s function. Methods: We u

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16

Shafiekhani, Azizollah, Sebastian Stach, Ştefan Ţălu, Senour Abdolghaderi, and Jahangir Bahmani. "3_D surface stereometry of Ag/DLC nanocomposite prepared by RF-PECVD." Results in Physics 15 (October 15, 2019): 1–8. https://doi.org/10.1016/j.rinp.2019.102731.

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In this study, a stereometric analysis of the three-dimensional (3-D) surfaces of the Ag/diamond-like carbon (DLC) nanocomposite films was done. The nanocomposite thin films were fabricated by Radio Frequency Plasma-Enhanced Chemical Vapour Deposition (RF-PECVD). The 3-D surface microtexture was studied by high-resolution Atomic Force Microscopy (AFM) records combined with statistical analyses. More detailed information about surface statistical parameters and topographic features of analyzed samples were performed. The statistical parameters relating to the segmented motifs consistent with IS

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17

Nadia Hasna, Safira Rizqi, and Mein Kharnolis. "Penerapan Motif Batik Papua dengan Teknik Bordir pada Busana Pengantin Wanita." BAJU: Journal of Fashion & Textile Design Unesa 2, no. 1 (2022): 18–23. http://dx.doi.org/10.26740/baju.v2n1.p18-23.

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Анотація:

Motif batik Papua yang berasal dari ragam hias khas Papua yang menjadi inspirasi dalam pembuatan busana pengantin wanita. Tujuan penelitian adalah untuk mengetahui proses dan hasil jadi penerapan motif batik papua dengan teknik bordir dibusana pengantin wanita. Metode yang digunakan adalah Double Diamond, yang terdiri dari 4 tahapan yaitu dicover, define, develop dan deliver. Dari hasil yang diperoleh, motif batik papua yaitu motif suku asmat yang diwujudkan teknik bordir digunakan sebagai detail di busana pengantin wanita. Proses pembuatan dengan cara membordir dengan mengikuti motif / pola y

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18

TASCHNER, Sabine, Andreas MEINKE, Alexander von GABAIN, and Aoife P. BOYD. "Selection of peptide entry motifs by bacterial surface display." Biochemical Journal 367, no. 2 (2002): 393–402. http://dx.doi.org/10.1042/bj20020164.

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Surface display technologies have been established previously to select peptides and polypeptides that interact with purified immobilized ligands. In the present study, we designed and implemented a surface display-based technique to identify novel peptide motifs that mediate entry into eukaryotic cells. An Escherichia coli library expressing surface-displayed peptides was combined with eukaryotic cells and the gentamicin protection assay was performed to select recombinant E. coli, which were internalized into eukaryotic cells by virtue of the displayed peptides. To establish the proof of pri

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19

Coleman, Scott H., Nanette Van Damme, John R. Day, et al. "Leucine-Specific, Functional Interactions between Human Immunodeficiency Virus Type 1 Nef and Adaptor Protein Complexes." Journal of Virology 79, no. 4 (2005): 2066–78. http://dx.doi.org/10.1128/jvi.79.4.2066-2078.2005.

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ABSTRACT The human immunodeficiency virus type 1 virulence protein Nef interacts with the endosomal sorting machinery via a leucine-based motif. Similar sequences within the cytoplasmic domains of cellular transmembrane proteins bind to the adaptor protein (AP) complexes of coated vesicles to modulate protein traffic, but the molecular basis of the interactions between these motifs and the heterotetrameric complexes is controversial. To identify the target of the Nef leucine motif, the native sequence was replaced with either leucine- or tyrosine-based AP-binding sequences from cellular protei

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20

Coelho, Miguel B., David B. Ascher, Clare Gooding, et al. "Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins." Biochemical Society Transactions 44, no. 4 (2016): 1058–65. http://dx.doi.org/10.1042/bst20160080.

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Polypyrimidine tract binding protein (PTBP1) is a heterogeneous nuclear ribonucleoprotein (hnRNP) that plays roles in most stages of the life-cycle of pre-mRNA and mRNAs in the nucleus and cytoplasm. PTBP1 has four RNA binding domains of the RNA recognition motif (RRM) family, each of which can bind to pyrimidine motifs. In addition, RRM2 can interact via its dorsal surface with proteins containing short peptide ligands known as PTB RRM2 interacting (PRI) motifs, originally found in the protein Raver1. Here we review our recent progress in understanding the interactions of PTB with RNA and wit

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21

Rahmawati, Septi. "Kucing Sebagai Motif Hias Batik Pada Kemeja Pria." Qualia: Jurnal Ilmiah Edukasi Seni Rupa dan Budaya Visual 3, no. 1 (2023): 30–35. https://doi.org/10.21009/qualia.31.05.

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Cats are friendly animals, they are sensitive to their surroundings, and sometimes their behavior attracts attention. This behavior became a source of inspiration in designing shirts with fabric made using the batik technique. The design method uses practice-based research. The shirt that will be made this time is a men's shirt with short sleeves, without pockets, and a variety of buttons covered by fabric. There are 3 steps in making a work, namely exploring motifs, designing the work, and evaluating the results. The results of the motif exploration obtained 4 motifs, namely the cat motif as

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22

Kurumatani, Natsumi, Hiroyuki Monji, and Takenao Ohkawa. "Binding Site Extraction by Similar Subgraphs Mining from Protein Molecular Surfaces and Its Application to Protein Classification." International Journal on Artificial Intelligence Tools 23, no. 03 (2014): 1460007. http://dx.doi.org/10.1142/s0218213014600070.

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Most proteins express their functions by binding with other proteins or molecular compounds (ligands). Since the characteristics of the local portion involved in binding (binding site) often determine the function of the protein, clarifying the location of the binding site of the protein helps analyze the function of proteins. Binding sites that bind to similar ligands often have common surface structures (surface motifs). Extracting the surface motifs among several proteins with similar functions improves binding site prediction. We propose a method that predicts binding sites by extracting t

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23

Satława, Tadeusz, Mateusz Tarkowski, Sonia Wróbel, et al. "LAP: Liability Antibody Profiler by sequence & structural mapping of natural and therapeutic antibodies." PLOS Computational Biology 20, no. 3 (2024): e1011881. http://dx.doi.org/10.1371/journal.pcbi.1011881.

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Antibody-based therapeutics must not undergo chemical modifications that would impair their efficacy or hinder their developability. A commonly used technique to de-risk lead biotherapeutic candidates annotates chemical liability motifs on their sequence. By analyzing sequences from all major sources of data (therapeutics, patents, GenBank, literature, and next-generation sequencing outputs), we find that almost all antibodies contain an average of 3–4 such liability motifs in their paratopes, irrespective of the source dataset. This is in line with the common wisdom that liability motif annot

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24

He, Bin, and Elizabeth M. Wilson. "Electrostatic Modulation in Steroid Receptor Recruitment of LXXLL and FXXLF Motifs." Molecular and Cellular Biology 23, no. 6 (2003): 2135–50. http://dx.doi.org/10.1128/mcb.23.6.2135-2150.2003.

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ABSTRACT Coactivator recruitment by activation function 2 (AF2) in the steroid receptor ligand binding domain takes place through binding of an LXXLL amphipathic α-helical motif at the AF2 hydrophobic surface. The androgen receptor (AR) and certain AR coregulators are distinguished by an FXXLF motif that interacts selectively with the AR AF2 site. Here we show that LXXLL and FXXLF motif interactions with steroid receptors are modulated by oppositely charged residues flanking the motifs and charge clusters bordering AF2 in the ligand binding domain. An increased number of charged residues flank

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25

Marks, M. S., L. Woodruff, H. Ohno, and J. S. Bonifacino. "Protein targeting by tyrosine- and di-leucine-based signals: evidence for distinct saturable components." Journal of Cell Biology 135, no. 2 (1996): 341–54. http://dx.doi.org/10.1083/jcb.135.2.341.

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Targeting of transmembrane proteins to lysosomes, endosomal compartments, or the trans-Golgi network is largely dependent upon cytoplasmically exposed sorting signals. Among the most widely used signals are those that conform to the tyrosine-based motif, YXXO (where Y is tyrosine, X is any amino acid, and O is an amino acid with a bulky hydrophobic group), and to the di-leucine (or LL) motif. Signals conforming to both motifs have been implicated in protein localization to similar post-Golgi compartments. We have exploited the saturability of sorting to ask whether different YXXO or LL signals

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26

Duffy, Josh, Bhargavi Patham, and Kojo Mensa-Wilmot. "Discovery of functional motifs in h-regions of trypanosome signal sequences." Biochemical Journal 426, no. 2 (2010): 135–45. http://dx.doi.org/10.1042/bj20091277.

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N-terminal signal peptides direct secretory proteins into the ER (endoplasmic reticulum) of eukaryotes or the periplasmic space of prokaryotes. A hydrophobic core (h-region) is important for signal sequence function; however, the mechanism of h-region action is not resolved. To gain new insight into signal sequences, bioinformatic analysis of h-regions from humans, Saccharomyces cerevisiae, Trypanosoma brucei and Escherichia coli was performed. Each species contains a unique set of peptide motifs (h-motifs) characterized by identity components (i.e. sequence of conserved amino acids) joined by

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27

Tong, Kit I., Balasundaram Padmanabhan, Akira Kobayashi, et al. "Different Electrostatic Potentials Define ETGE and DLG Motifs as Hinge and Latch in Oxidative Stress Response." Molecular and Cellular Biology 27, no. 21 (2007): 7511–21. http://dx.doi.org/10.1128/mcb.00753-07.

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ABSTRACT Nrf2 is the regulator of the oxidative/electrophilic stress response. Its turnover is maintained by Keap1-mediated proteasomal degradation via a two-site substrate recognition mechanism in which two Nrf2-Keap1 binding sites form a hinge and latch. The E3 ligase adaptor Keap1 recognizes Nrf2 through its conserved ETGE and DLG motifs. In this study, we examined how the ETGE and DLG motifs bind to Keap1 in a very similar fashion but with different binding affinities by comparing the crystal complex of a Keap1-DC domain-DLG peptide with that of a Keap1-DC domain-ETGE peptide. We found tha

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28

Novakovic, Sinisa, Earl T. Sawai, and Kathryn Radke. "Dileucine and YXXL Motifs in the Cytoplasmic Tail of the Bovine Leukemia Virus Transmembrane Envelope Protein Affect Protein Expression on the Cell Surface." Journal of Virology 78, no. 15 (2004): 8301–11. http://dx.doi.org/10.1128/jvi.78.15.8301-8311.2004.

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ABSTRACT Several retroviruses downmodulate the cell surface expression of envelope (Env) proteins through peptide sequences located in the cytoplasmic tail of the transmembrane (TM) subunit. We investigated whether cell surface expression of a chimeric protein containing the cytoplasmic domain of the TM protein (CTM) of bovine leukemia virus (BLV) was regulated by two membrane-proximal dileucine motifs or by tyrosine Y487 or Y498 in YXXL motifs. A chimeric protein composed of the extracellular and membrane-spanning portions of human CD8-α plus a wild-type (wt) BLV CTM was detectable on the sur

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29

Shmulevitz, Maya, Jayme Salsman, and Roy Duncan. "Palmitoylation, Membrane-Proximal Basic Residues, and Transmembrane Glycine Residues in the Reovirus p10 Protein Are Essential for Syncytium Formation." Journal of Virology 77, no. 18 (2003): 9769–79. http://dx.doi.org/10.1128/jvi.77.18.9769-9779.2003.

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ABSTRACT Avian reovirus and Nelson Bay reovirus are two unusual nonenveloped viruses that induce extensive cell-cell fusion via expression of a small nonstructural protein, termed p10. We investigated the importance of the transmembrane domain, a conserved membrane-proximal dicysteine motif, and an endodomain basic region in the membrane fusion activity of p10. We now show that the p10 dicysteine motif is palmitoylated and that loss of palmitoylation correlates with a loss of fusion activity. Mutational and functional analyses also revealed that a triglycine motif within the transmembrane doma

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30

Lai, Mei-Hsiu, Nicholas E. Clay, Dong Hyun Kim, and Hyunjoon Kong. "Bacteria-mimicking nanoparticle surface functionalization with targeting motifs." Nanoscale 7, no. 15 (2015): 6737–44. http://dx.doi.org/10.1039/c5nr00736d.

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31

Panseri, Silvia, Laura Russo, Monica Montesi, et al. "Bioactivity of surface tethered Osteogenic Growth Peptide motifs." MedChemComm 5, no. 7 (2014): 899. http://dx.doi.org/10.1039/c4md00112e.

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32

Petersen, Helen J., Dorothea O. Tilley, Jennifer Haworth, et al. "Multiple sites on Streptococcus gordonii surface protein PadA bind to platelet GPIIbIIIa." Thrombosis and Haemostasis 110, no. 12 (2013): 1278–87. http://dx.doi.org/10.1160/th13-07-0580.

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SummaryInfective endocarditis is a life threatening disease caused by a bacterial infection of the endocardial surfaces of the heart. The oral pathogen, Streptococcus gordonii is amongst the most common pathogens isolated from infective endocarditis patients. Previously we identified a novel cell wall protein expressed on S. gordonii called platelet adherence protein A (PadA) that specifically interacts with platelet GPIIb/IIIa. The interaction between PadA and GPIIb/IIIa resulted in firm platelet adhesion, dense granule secretion and platelet spreading on immobilised S. gordonii. This study s

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33

Krishnan, Arun, Kuo-Bin Li, and Praveen Issac. "Rapid Detection of Conserved Regions in Protein Sequences Using Wavelets." In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation 4, no. 2 (2004): 133–48. https://doi.org/10.3233/isb-00123.

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We present an algorithm to detect protein sub-structural motifs from primary sequence. The input to the algorithm is a set of aligned multiple protein sequences. It uses wavelet transforms to decompose protein sequences represented numerically by different indices (such as polarity, accessible surface area or electron-ion integration potentials of the amino acids). The numerical representation of a protein sequence has significant correlation with its biological activity, thus common motifs are expected to be observable from the wavelet spectrum. The decomposed signals are then up-sampled and

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34

Ilinskaya, Anna, Gisela Heidecker, and David Derse. "Opposing Effects of a Tyrosine-Based Sorting Motif and a PDZ-Binding Motif Regulate Human T-Lymphotropic Virus Type 1 Envelope Trafficking." Journal of Virology 84, no. 14 (2010): 6995–7004. http://dx.doi.org/10.1128/jvi.01853-09.

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ABSTRACT Human T-lymphotropic virus type 1 (HTLV-1) envelope (Env) glycoprotein mediates binding of the virus to its receptor on the surface of target cells and subsequent fusion of virus and cell membranes. To better understand the mechanisms that control HTLV-1 Env trafficking and activity, we have examined two protein-protein interaction motifs in the cytoplasmic domain of Env. One is the sequence YSLI, which matches the consensus YXXΦ motifs that are known to interact with various adaptor protein complexes; the other is the sequence ESSL at the C terminus of Env, which matches the consensu

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35

He, Tengfei, and Xiao Zhou. "MotifGPL: Motif-Enhanced Graph Prototype Learning for Deciphering Urban Social Segregation." Proceedings of the AAAI Conference on Artificial Intelligence 39, no. 27 (2025): 28079–87. https://doi.org/10.1609/aaai.v39i27.35026.

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Social segregation in cities, spanning racial, residential, and income dimensions, is becoming increasingly diverse and severe. As urban spaces and social dynamics grow more complex, residents experience varying levels of segregation, which, if left unaddressed, could exacerbate crime rates, fuel social tensions, and lead to other societal challenges. Effectively addressing these issues requires a comprehensive analysis of the underlying structures of urban spaces and resident interactions. While previous studies have primarily focused on surface-level indicators of segregation, they often fai

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36

Pechenart, Pierre-Philip, Margaux Gillet, and Marc Mimram. "Etude sur la déformabilité de la nappe." SHS Web of Conferences 47 (2018): 01017. http://dx.doi.org/10.1051/shsconf/20184701017.

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Cet article vise à explorer la déformabilité d’une nappe plane découpée par un motif. Ce dernier lui donne la capacité de subir des déformations, d’acquérir de la souplesse tout en conservant un continu de matière, et d’évoluer d’une surface plane à une surface complexe –voire à double courbure. Les notions de surface, de surface développable, et de nappe architecturale forment les bases de l’étude du motif et de son fonctionnement. L’étude du fonctionnement d’une poutre entre deux appuis permet de simplifier notre approche, notamment dans l’analyse de ses déformations, de sa résistance au cis

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37

Lungu, A., L. Gurău, S. Georgescu, and C. Coşereanu. "Computer-aided methods for furniture decoration with traditional motifs of textile heritage." IOP Conference Series: Materials Science and Engineering 1235, no. 1 (2022): 012041. http://dx.doi.org/10.1088/1757-899x/1235/1/012041.

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Abstract The present paper introduces computer-aided methods for the transposition of ornaments inspired from the textile heritage into the surface furniture decoration. Using digital technology, the furniture industry may bring into modern life the traditional motifs, contributing thus to the preservation of the cultural heritage from the region Ţara Bârsei, located in Transylvania. Two motifs inspired by the traditional costumes from South-Eastern Transylvania were digitized using CorelDraw software. They were imported in AutoCAD and the information was transferred both to CNC router and las

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38

Zähner, Dorothea, and Regine Hakenbeck. "The Streptococcus pneumoniaeBeta-Galactosidase Is a Surface Protein." Journal of Bacteriology 182, no. 20 (2000): 5919–21. http://dx.doi.org/10.1128/jb.182.20.5919-5921.2000.

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ABSTRACT The β-galactosidase gene of Streptococcus pneumoniae,bgaA, encodes a putative 2,235-amino-acid protein with the two amino acid motifs characteristic of the glycosyl hydrolase family of proteins. In addition, an N-terminal signal sequence and a C-terminal LPXTG motif typical of surface-associated proteins of gram-positive bacteria are present. Trypsin treatment of cells resulted in solubilization of the enzyme, documenting that it is associated with the cell envelope. In order to obtain defined mutants suitable forlacZ reporter experiments, the bgaA gene was disrupted, resulting in a c

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39

Bakhos-Douaihy, Dalal, Elie Seaayfan, Nadia Frachon, Sylvie Demaretz, Martin Kömhoff, and Kamel Laghmani. "Diacidic Motifs in the Carboxyl Terminus Are Required for ER Exit and Translocation to the Plasma Membrane of NKCC2." International Journal of Molecular Sciences 23, no. 21 (2022): 12761. http://dx.doi.org/10.3390/ijms232112761.

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Mutations in the apical Na-K-2Cl co-transporter, NKCC2, cause type I Bartter syndrome (BS1), a life-threatening kidney disease. We have previously demonstrated that the BS1 variant Y998X, which deprives NKCC2 from its highly conserved dileucine-like motifs, compromises co-transporter surface delivery through ER retention mechanisms. However, whether these hydrophobic motifs are sufficient for anterograde trafficking of NKCC2 remains to be determined. Interestingly, sequence analysis of NKCC2 C-terminus revealed the presence of consensus di-acidic (D/E-X-D/E) motifs, 949EEE951 and 1019DAELE1023

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40

Johnson, Amy O., Michael A. Lampson, and Timothy E. McGraw. "A Di-Leucine Sequence and a Cluster of Acidic Amino Acids Are Required for Dynamic Retention in the Endosomal Recycling Compartment of Fibroblasts." Molecular Biology of the Cell 12, no. 2 (2001): 367–81. http://dx.doi.org/10.1091/mbc.12.2.367.

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Insulin-regulated aminopeptidase (IRAP), a transmembrane aminopeptidase, is dynamically retained within the endosomal compartment of fibroblasts. The characteristics of this dynamic retention are rapid internalization from the plasma membrane and slow recycling back to the cell surface. These specialized trafficking kinetics result in <15% of IRAP on the cell surface at steady state, compared with 35% of the transferrin receptor, another transmembrane protein that traffics between endosomes and the cell surface. Here we demonstrate that a 29-amino acid region of IRAP's cytoplasmic domain (r

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41

Hasegawa, Atsushi, Ritsuko Shimizu, Hirofumi Kurokawa, and Masayuki Yamamoto. "DNA Binding Diversity Achieved Through the Interaction of GATA1 N-Finger and GATA Motif Is Important for Embryonic Erythropoiesis." Blood 120, no. 21 (2012): 3441. http://dx.doi.org/10.1182/blood.v120.21.3441.3441.

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Abstract Abstract 3441 Transcription factor GATA1 regulates a set of genes essential for the erythroid and megakaryocytic cell differentiation through the interaction with GATA motifs (consensus sequence: A/TGATAA/T). Two zinc fingers within GATA1 have been identified to be important in the DNA binding of GATA1, which are referred to as C-finger (CF) and N-finger (NF) domains. It has been shown that transactivation activity of GATA1 is completely abolished upon deletion of the CF domain, indicating that the CF domain is a requisite for the DNA binding of GATA1. While conventional reporter tran

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42

Sangeetha, Ramalingam, Kasthuri Balasubramani, Kaliyaperumal Thanigaimani, and Savaridasson Jose Kavitha. "Crystal structure and Hirshfeld surface analysis of 2,4-diamino-6-phenyl-1,3,5-triazin-1-ium 4-methylbenzenesulfonate." Acta Crystallographica Section E Crystallographic Communications 74, no. 8 (2018): 1159–62. http://dx.doi.org/10.1107/s2056989018010368.

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In the title molecular salt, C9H10N5 +·C7H7O3S−, the asymmetric unit consists of a 2,4-diamino-6-phenyl-1,3,5-triazin-1-ium cation and a 4-methylbenzenesulfonate anion. The cation is protonated at the N atom lying between the amine and phenyl substituents. The protonated N and amino-group N atoms are involved in hydrogen bonding with the sulfonate O atoms through a pair of intermolecular N—H...O hydrogen bonds, giving rise to a hydrogen-bonded cyclic motif with R 2 2(8) graph-set notation. The inversion-related molecules are further linked by four N—H...O intermolecular interactions to produce

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43

Gottwein, Eva, Jochen Bodem, Barbara Müller, Ariane Schmechel, Hanswalter Zentgraf, and Hans-Georg Kräusslich. "The Mason-Pfizer Monkey Virus PPPY and PSAP Motifs Both Contribute to Virus Release." Journal of Virology 77, no. 17 (2003): 9474–85. http://dx.doi.org/10.1128/jvi.77.17.9474-9485.2003.

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ABSTRACT Late (L) domains are required for the efficient release of several groups of enveloped viruses. Three amino acid motifs have been shown to provide L-domain function, namely, PPXY, PT/SAP, or YPDL. The retrovirus Mason-Pfizer monkey virus (MPMV) carries closely spaced PPPY and PSAP motifs. Mutation of the PPPY motif results in a complete loss of virus release. Here, we show that the PSAP motif acts as an additional L domain and promotes the efficient release of MPMV but requires an intact PPPY motif to perform its function. Examination of HeLaP4 cells expressing PSAP mutant virus by el

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44

Sheshadri, S. N., C. S. Chidan Kumar, S. Naveen, M. K. Veeraiah, Kakarla Raghava Reddy, and Ismail Warad. "Crystal structure and Hirshfeld surface analysis of 2-(4-nitrophenyl)-2-oxoethyl benzoate." Acta Crystallographica Section E Crystallographic Communications 75, no. 11 (2019): 1719–23. http://dx.doi.org/10.1107/s2056989019013975.

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The title compound, C15H11NO5, is relatively planar, with the planes of the two aromatic rings being inclined to each other by 3.09 (5)°. In the crystal, molecules are linked by a pair of C—H...O hydrogen bonds, forming inversion dimers, which enclose an R 2 2(16) ring motif. The dimers are linked by a further pair of C—H...O hydrogen-bonds forming ribbons enclosing R 4 4(26) ring motifs. The ribbons are linked by offset π–π interactions [centroid–centroid distances = 3.6754 (6)–3.7519 (6) Å] to form layers parallel to the ac plane. Through Hirshfeld surface analyses, the d norm surfaces, elec

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45

Takeda, Tetsuro, Hajime Yamazaki, and Marilyn G. Farquhar. "Identification of an apical sorting determinant in the cytoplasmic tail of megalin." American Journal of Physiology-Cell Physiology 284, no. 5 (2003): C1105—C1113. http://dx.doi.org/10.1152/ajpcell.00514.2002.

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Megalin is the main endocytic receptor of the proximal tubule and is responsible for reabsorption of many filtered proteins. In contrast to other members of the low-density lipoprotein (LDL) receptor gene family, it is expressed on the apical plasma membrane (PM) of polarized epithelial cells. To identify megalin's apical sorting signal, we generated deletion mutants and chimeric minireceptors composed of complementary regions of megalin and LDL receptor-related protein (LRP) and assessed the distribution of the mutants in Madin-Darby canine kidney (MDCK) cells by immunofluorescence and cell s

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46

Boonen, Marielle, Roberta Rezende de Castro, Gaëlle Cuvelier, Isabelle Hamer, and Michel Jadot. "A dileucine signal situated in the C-terminal tail of the lysosomal membrane protein p40 is responsible for its targeting to lysosomes." Biochemical Journal 414, no. 3 (2008): 431–40. http://dx.doi.org/10.1042/bj20071626.

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Transport of newly synthesized lysosomal membrane proteins from the TGN (trans-Golgi network) to the lysosomes is due to the presence of specific signals in their cytoplasmic domains that are recognized by cytosolic adaptors. p40, a hypothetical transporter of 372 amino acids localized in the lysosomal membrane, contains four putative lysosomal sorting motifs in its sequence: three of the YXXϕ-type (Y6QLF, Y106VAL, Y333NGL) and one of the [D/E]XXXL[L/I]-type (EQERL360L361). To test the role of these motifs in the biosynthetic transport of p40, we replaced the most critical residues of these co

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47

Adamkiewicz, Malgorzata, David O’Hagan, and Georg Hähner. "Organic chemistry on surfaces: Direct cyclopropanation by dihalocarbene addition to vinyl terminated self-assembled monolayers (SAMs)." Beilstein Journal of Organic Chemistry 10 (December 5, 2014): 2897–902. http://dx.doi.org/10.3762/bjoc.10.307.

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C11-Vinyl-terminated self-assembled monolayers (SAMs) on silica surfaces are successfully modified in C–C bond forming reactions with dihalocarbenes to generate SAMs, terminated with dihalo- (fluoro, chloro, bromo) cyclopropane motifs with about 30% surface coverage.

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48

Mitchell, Richard S., Rittik Chaudhuri, O. Wolf Lindwasser, et al. "Competition Model for Upregulation of the Major Histocompatibility Complex Class II-Associated Invariant Chain by Human Immunodeficiency Virus Type 1 Nef." Journal of Virology 82, no. 16 (2008): 7758–67. http://dx.doi.org/10.1128/jvi.02668-07.

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ABSTRACT The human immunodeficiency virus type 1 (HIV-1) Nef protein upregulates the expression of the invariant chain (Ii)/major histocompatibility complex class II (MHC-II) complex at the cell surface. This complex appears to reach the antigen-loading endosomal compartment at least in part via an indirect pathway in which it is internalized from the cell surface via the adaptor protein 2 (AP-2) complex. Here we provide evidence for a competition model to explain how Nef upregulates the expression of Ii at the cell surface. In this model, Nef and Ii compete for binding to AP-2. In support of

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49

Coblitz, Brian, Sojin Shikano, Meng Wu, et al. "C-terminal Recognition by 14-3-3 Proteins for Surface Expression of Membrane Receptors." Journal of Biological Chemistry 280, no. 43 (2005): 36263–72. http://dx.doi.org/10.1074/jbc.m507559200.

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Diverse functions of 14-3-3 proteins are directly coupled to their ability to interact with targeted peptide substrates. RSX(pS/pT)XP and RXΦX(pS/pT)XP are two canonical consensus binding motifs for 14-3-3 proteins representing the two common binding modes, modes I and II, between 14-3-3 and internal peptides. Using a genetic selection, we have screened a random peptide library and identified a group of C-terminal motifs, termed SWTY, capable of overriding an endoplasmic reticulum localization signal and redirecting membrane proteins to cell surface. Here we report that the C-terminal SWTY mot

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Muhammad Yasir, Fitria Wardani, Apliniari Yuniar, and Ardhansyah Putra Hrp. "PEMBERDAYAAN MASYARAKAT MELALUI INOVASI BATIK DAN PRODUK MAKANAN MANGROVE DI DESA TANJUNG REJO KECAMATAN PERCUT SEI TUAN KABUPATEN DELI SERDANG." J-ABDI: Jurnal Pengabdian kepada Masyarakat 1, no. 9 (2022): 2157–62. http://dx.doi.org/10.53625/jabdi.v1i9.1252.

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Mangroves are typical plants found in coastal areas. Mangrove batik motifs as coastal plants have not been exposed optimally. Meanwhile, the coastal environment with its flora and fauna has tremendous potential as a batik motif. Aside from being a motif, mangrove plants can also be used as natural batik dyes and mangroves can be processed into food and beverage ingredients which are currently becoming a trend in the community. The use of mangroves as natural dyes, in addition to providing natural colors and beautiful motifs, can also reduce environmental pollution. The method of implementing t

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